I know how to create a symbolic link in windows in a .bat script:
mklink /J  
  How to do the sam
Here is a project that has the PInvoke signatures for creating junctions: http://www.codeproject.com/Articles/15633/Manipulating-NTFS-Junction-Points-in-NET. The code is copied below:
using System;
using System.IO;
using System.Runtime.InteropServices;
using System.Text;
using Microsoft.Win32.SafeHandles;
namespace Util {
    /// 
    /// Provides access to NTFS junction points in .Net.
    ///  
    public static class JunctionPoint {
        /// 
        /// The file or directory is not a reparse point.
        ///  
        private const int ERROR_NOT_A_REPARSE_POINT = 4390;
        /// 
        /// The reparse point attribute cannot be set because it conflicts with an existing attribute.
        ///  
        private const int ERROR_REPARSE_ATTRIBUTE_CONFLICT = 4391;
        /// 
        /// The data present in the reparse point buffer is invalid.
        ///  
        private const int ERROR_INVALID_REPARSE_DATA = 4392;
        /// 
        /// The tag present in the reparse point buffer is invalid.
        ///  
        private const int ERROR_REPARSE_TAG_INVALID = 4393;
        /// 
        /// There is a mismatch between the tag specified in the request and the tag present in the reparse point.
        ///  
        private const int ERROR_REPARSE_TAG_MISMATCH = 4394;
        /// 
        /// Command to set the reparse point data block.
        ///  
        private const int FSCTL_SET_REPARSE_POINT = 0x000900A4;
        /// 
        /// Command to get the reparse point data block.
        ///  
        private const int FSCTL_GET_REPARSE_POINT = 0x000900A8;
        /// 
        /// Command to delete the reparse point data base.
        ///  
        private const int FSCTL_DELETE_REPARSE_POINT = 0x000900AC;
        /// 
        /// Reparse point tag used to identify mount points and junction points.
        ///  
        private const uint IO_REPARSE_TAG_MOUNT_POINT = 0xA0000003;
        /// 
        /// This prefix indicates to NTFS that the path is to be treated as a non-interpreted
        /// path in the virtual file system.
        ///  
        private const string NonInterpretedPathPrefix = @"\??\";
        [Flags]
        private enum EFileAccess : uint {
            GenericRead = 0x80000000,
            GenericWrite = 0x40000000,
            GenericExecute = 0x20000000,
            GenericAll = 0x10000000,
        }
        [Flags]
        private enum EFileShare : uint {
            None = 0x00000000,
            Read = 0x00000001,
            Write = 0x00000002,
            Delete = 0x00000004,
        }
        private enum ECreationDisposition : uint {
            New = 1,
            CreateAlways = 2,
            OpenExisting = 3,
            OpenAlways = 4,
            TruncateExisting = 5,
        }
        [Flags]
        private enum EFileAttributes : uint {
            Readonly = 0x00000001,
            Hidden = 0x00000002,
            System = 0x00000004,
            Directory = 0x00000010,
            Archive = 0x00000020,
            Device = 0x00000040,
            Normal = 0x00000080,
            Temporary = 0x00000100,
            SparseFile = 0x00000200,
            ReparsePoint = 0x00000400,
            Compressed = 0x00000800,
            Offline = 0x00001000,
            NotContentIndexed = 0x00002000,
            Encrypted = 0x00004000,
            Write_Through = 0x80000000,
            Overlapped = 0x40000000,
            NoBuffering = 0x20000000,
            RandomAccess = 0x10000000,
            SequentialScan = 0x08000000,
            DeleteOnClose = 0x04000000,
            BackupSemantics = 0x02000000,
            PosixSemantics = 0x01000000,
            OpenReparsePoint = 0x00200000,
            OpenNoRecall = 0x00100000,
            FirstPipeInstance = 0x00080000
        }
        [StructLayout(LayoutKind.Sequential)]
        private struct REPARSE_DATA_BUFFER {
            /// 
            /// Reparse point tag. Must be a Microsoft reparse point tag.
            ///  
            public uint ReparseTag;
            /// 
            /// Size, in bytes, of the data after the Reserved member. This can be calculated by:
            /// (4 * sizeof(ushort)) + SubstituteNameLength + PrintNameLength + 
            /// (namesAreNullTerminated ? 2 * sizeof(char) : 0);
            ///  
            public ushort ReparseDataLength;
            /// 
            /// Reserved; do not use. 
            ///  
            public ushort Reserved;
            /// 
            /// Offset, in bytes, of the substitute name string in the PathBuffer array.
            ///  
            public ushort SubstituteNameOffset;
            /// 
            /// Length, in bytes, of the substitute name string. If this string is null-terminated,
            /// SubstituteNameLength does not include space for the null character.
            ///  
            public ushort SubstituteNameLength;
            /// 
            /// Offset, in bytes, of the print name string in the PathBuffer array.
            ///  
            public ushort PrintNameOffset;
            /// 
            /// Length, in bytes, of the print name string. If this string is null-terminated,
            /// PrintNameLength does not include space for the null character. 
            ///  
            public ushort PrintNameLength;
            /// 
            /// A buffer containing the unicode-encoded path string. The path string contains
            /// the substitute name string and print name string.
            ///  
            [MarshalAs(UnmanagedType.ByValArray, SizeConst = 0x3FF0)]
            public byte[] PathBuffer;
        }
        [DllImport("kernel32.dll", CharSet = CharSet.Auto, SetLastError = true)]
        private static extern bool DeviceIoControl(IntPtr hDevice, uint dwIoControlCode,
            IntPtr InBuffer, int nInBufferSize,
            IntPtr OutBuffer, int nOutBufferSize,
            out int pBytesReturned, IntPtr lpOverlapped);
        [DllImport("kernel32.dll", SetLastError = true)]
        private static extern IntPtr CreateFile(
            string lpFileName,
            EFileAccess dwDesiredAccess,
            EFileShare dwShareMode,
            IntPtr lpSecurityAttributes,
            ECreationDisposition dwCreationDisposition,
            EFileAttributes dwFlagsAndAttributes,
            IntPtr hTemplateFile);
        /// 
        /// Creates a junction point from the specified directory to the specified target directory.
        ///  
        /// 
        /// Only works on NTFS.
        ///  
        /// The target directory to create
        /// The source directory to alias
        /// If true overwrites an existing reparse point or empty directory
        /// Thrown when the junction point could not be created or when
        /// an existing directory was found and  
        public static void Create(string sourceDir, string targetDir, bool overwrite) {
            sourceDir = Path.GetFullPath(sourceDir);
            if (!Directory.Exists(sourceDir))
                throw new IOException($"Source path does not exist or is not a directory.");
            if (Directory.Exists(targetDir))
                throw new IOException($"Directory '{targetDir}' already exists.");
            Directory.CreateDirectory(targetDir);
            using (SafeFileHandle handle = OpenReparsePoint(targetDir, EFileAccess.GenericWrite)) {
                byte[] sourceDirBytes = Encoding.Unicode.GetBytes(NonInterpretedPathPrefix + Path.GetFullPath(sourceDir));
                REPARSE_DATA_BUFFER reparseDataBuffer = new REPARSE_DATA_BUFFER();
                reparseDataBuffer.ReparseTag = IO_REPARSE_TAG_MOUNT_POINT;
                reparseDataBuffer.ReparseDataLength = (ushort)(sourceDirBytes.Length + 12);
                reparseDataBuffer.SubstituteNameOffset = 0;
                reparseDataBuffer.SubstituteNameLength = (ushort)sourceDirBytes.Length;
                reparseDataBuffer.PrintNameOffset = (ushort)(sourceDirBytes.Length + 2);
                reparseDataBuffer.PrintNameLength = 0;
                reparseDataBuffer.PathBuffer = new byte[0x3ff0];
                Array.Copy(sourceDirBytes, reparseDataBuffer.PathBuffer, sourceDirBytes.Length);
                int inBufferSize = Marshal.SizeOf(reparseDataBuffer);
                IntPtr inBuffer = Marshal.AllocHGlobal(inBufferSize);
                try {
                    Marshal.StructureToPtr(reparseDataBuffer, inBuffer, false);
                    int bytesReturned;
                    bool result = DeviceIoControl(handle.DangerousGetHandle(), FSCTL_SET_REPARSE_POINT,
                        inBuffer, sourceDirBytes.Length + 20, IntPtr.Zero, 0, out bytesReturned, IntPtr.Zero);
                    if (!result)
                        ThrowLastWin32Error($"Unable to create junction point '{sourceDir}' -> '{targetDir}'.");
                } finally {
                    Marshal.FreeHGlobal(inBuffer);
                }
            }
        }
        /// 
        /// Deletes a junction point at the specified source directory along with the directory itself.
        /// Does nothing if the junction point does not exist.
        ///  
        /// 
        /// Only works on NTFS.
        ///  
        /// The junction point path
        public static void Delete(string junctionPoint) {
            if (!Directory.Exists(junctionPoint)) {
                if (File.Exists(junctionPoint))
                    throw new IOException("Path is not a junction point.");
                return;
            }
            using (SafeFileHandle handle = OpenReparsePoint(junctionPoint, EFileAccess.GenericWrite)) {
                REPARSE_DATA_BUFFER reparseDataBuffer = new REPARSE_DATA_BUFFER();
                reparseDataBuffer.ReparseTag = IO_REPARSE_TAG_MOUNT_POINT;
                reparseDataBuffer.ReparseDataLength = 0;
                reparseDataBuffer.PathBuffer = new byte[0x3ff0];
                int inBufferSize = Marshal.SizeOf(reparseDataBuffer);
                IntPtr inBuffer = Marshal.AllocHGlobal(inBufferSize);
                try {
                    Marshal.StructureToPtr(reparseDataBuffer, inBuffer, false);
                    int bytesReturned;
                    bool result = DeviceIoControl(handle.DangerousGetHandle(), FSCTL_DELETE_REPARSE_POINT,
                        inBuffer, 8, IntPtr.Zero, 0, out bytesReturned, IntPtr.Zero);
                    if (!result)
                        ThrowLastWin32Error("Unable to delete junction point.");
                } finally {
                    Marshal.FreeHGlobal(inBuffer);
                }
                try {
                    Directory.Delete(junctionPoint);
                } catch (IOException ex) {
                    throw new IOException("Unable to delete junction point.", ex);
                }
            }
        }
        /// 
        /// Determines whether the specified path exists and refers to a junction point.
        ///  
        /// The junction point path
        /// True if the specified path represents a junction point 
        /// Thrown if the specified path is invalid
        /// or some other error occurs 
        public static bool Exists(string path) {
            if (!Directory.Exists(path))
                return false;
            using (SafeFileHandle handle = OpenReparsePoint(path, EFileAccess.GenericRead)) {
                string target = InternalGetTarget(handle);
                return target != null;
            }
        }
        /// 
        /// Gets the target of the specified junction point.
        ///  
        /// 
        /// Only works on NTFS.
        ///  
        /// The junction point path
        /// The target of the junction point 
        /// Thrown when the specified path does not
        /// exist, is invalid, is not a junction point, or some other error occurs 
        public static string GetTarget(string junctionPoint) {
            using (SafeFileHandle handle = OpenReparsePoint(junctionPoint, EFileAccess.GenericRead)) {
                string target = InternalGetTarget(handle);
                if (target == null)
                    throw new IOException("Path is not a junction point.");
                return target;
            }
        }
        private static string InternalGetTarget(SafeFileHandle handle) {
            int outBufferSize = Marshal.SizeOf(typeof(REPARSE_DATA_BUFFER));
            IntPtr outBuffer = Marshal.AllocHGlobal(outBufferSize);
            try {
                int bytesReturned;
                bool result = DeviceIoControl(handle.DangerousGetHandle(), FSCTL_GET_REPARSE_POINT,
                    IntPtr.Zero, 0, outBuffer, outBufferSize, out bytesReturned, IntPtr.Zero);
                if (!result) {
                    int error = Marshal.GetLastWin32Error();
                    if (error == ERROR_NOT_A_REPARSE_POINT)
                        return null;
                    ThrowLastWin32Error("Unable to get information about junction point.");
                }
                REPARSE_DATA_BUFFER reparseDataBuffer = (REPARSE_DATA_BUFFER)
                    Marshal.PtrToStructure(outBuffer, typeof(REPARSE_DATA_BUFFER));
                if (reparseDataBuffer.ReparseTag != IO_REPARSE_TAG_MOUNT_POINT)
                    return null;
                string targetDir = Encoding.Unicode.GetString(reparseDataBuffer.PathBuffer,
                    reparseDataBuffer.SubstituteNameOffset, reparseDataBuffer.SubstituteNameLength);
                if (targetDir.StartsWith(NonInterpretedPathPrefix))
                    targetDir = targetDir.Substring(NonInterpretedPathPrefix.Length);
                return targetDir;
            } finally {
                Marshal.FreeHGlobal(outBuffer);
            }
        }
        private static SafeFileHandle OpenReparsePoint(string reparsePoint, EFileAccess accessMode) {
            SafeFileHandle reparsePointHandle = new SafeFileHandle(CreateFile(reparsePoint, accessMode,
                EFileShare.Read | EFileShare.Write | EFileShare.Delete,
                IntPtr.Zero, ECreationDisposition.OpenExisting,
                EFileAttributes.BackupSemantics | EFileAttributes.OpenReparsePoint, IntPtr.Zero), true);
            if (Marshal.GetLastWin32Error() != 0)
                ThrowLastWin32Error("Unable to open reparse point.");
            return reparsePointHandle;
        }
        private static void ThrowLastWin32Error(string message) {
            throw new IOException(message, Marshal.GetExceptionForHR(Marshal.GetHRForLastWin32Error()));
        }
    }
}