I have the following piece of msbuild code:
  
    C:\\DirA\\ 
    C:\\DirB\\ 
  
         Yes, what you want is called batching in MSBuild. The
;%(Dirs.Identity)
Defined in the Outputs will cause this task to be executed for each item in the Dirs ItemGroup.
<?xml version="1.0" encoding="utf-8"?>
<Project DefaultTargets="CopyFiles"
   xmlns="http://schemas.microsoft.com/developer/msbuild/2003" 
   ToolsVersion="3.5">
<ItemGroup>
    <Dirs Include="C:\DirA" />
    <Dirs Include="C:\DirB" />
</ItemGroup>
<Target Name="CopyFiles"
    Inputs="@(FilesToCopy);@(Dirs)"
    Outputs="@(FilesToCopy -> '%(Dirs.Identity)%(Filename)%(Extension)');%(Dirs.Identity)" >
    <Message Text="%(Dirs.Identity)" />
</Target>
</Project>
Outputs:
Build started 8/19/2009 10:11:57 PM.
Project "D:\temp\test.proj" on node 0 (default targets).
  C:\DirA
CopyFiles:
  C:\DirB
Done Building Project "D:\temp\test.proj" (default targets).
Change the Message task to Copy task with the following condition and you are done:
Condition="Exists('%(Dirs.Identity)') AND '@(FilesToCopy)' != ''"
You should be able to generate an ItemGroup containing the Dirs and then % on that.
<ItemGroup>
    <Dirs Include="C:\DirA\;C:\DirB\">
</ItemGroup>
<Target Name="CopyFiles"
    Condition="Exists('%(Dirs)') AND '@(FilesToCopy)' != ''"
    Inputs="@(FilesToCopy)"
    Outputs="@(FilesToCopy -> '%(Dirs)%(Filename)%(Extension)')">
    <Copy SourceFiles="@(FilesToCopy)" DestinationFolder="%(Dirs)" />
</Target>
Or you can do 2 explicit calls:
<Target Name="CopyFiles">
    <MsBuild Projects="$(MSBuildProjectFullPath)" Targets="CopyASetOfFiles" Properties="FilesToCopy=@(FilesToCopy);DestDir=$(DirA)" />
    <MsBuild Projects="$(MSBuildProjectFullPath)" Targets="CopyASetOfFiles" Properties="FilesToCopy=@(FilesToCopy);DestDir=$(DirB)" />
</Target>
<Target Name="CopyASetOfFiles"
    Condition="Exists('$(DestDir)') AND '@(FilesToCopy)' != ''"
    Inputs="@(FilesToCopy)"
    Outputs="@(FilesToCopy -> '$(DestDir)%(Filename)%(Extension)')">
    <Copy SourceFiles="@(FilesToCopy)" DestinationFolder="$(DestDir)" />
</Target>
I haven't tested either syntax, but am relatively more confident of the second.
(The answer, if there is one, is in my Sayed Hashimi book on my desk - you'll have to wait until the first of:
As someone already mentiond the answer is batching.
Here are some links: