I have started a new project in Xcode by duplicating an existing folder, because my new app will have a lot of common features with the old one.
The problem is that
If you need to remove a lot of files, you could create User-Defined Build Setting which should be called EXCLUDED_SOURCE_FILE_NAMES. And add file names or patterns.
In my case I selected the target I wanted to omit some files, Editor -> Add Build Setting -> Add User-Defined Setting (at first this is greyed out somehow. I selected the project file (just above TARGETS) then reselected target file and was able to create User-Defined Setting) -> name it EXCLUDED_SOURCE_FILE_NAMES -> value something like PREFIX*
Of course you can create User-Defined Setting for whole project that way all targets will have it.
Example how it may look:

Original answer: http://lists.apple.com/archives/xcode-users/2009/Jun/msg00153.html