I don't use win32, but it might be helpful if you would detail what sort of program the c# is,( for example: an executable that takes a file as input and delivers it processed to stdout? ) If that is the case, you can probably use a Perl IPC module, like IPC::Run , IPC::Open3, etc. Read "perldoc perlipc" for the general idea. You open your program thru pipes or sockets, send it input, and collect output. The key issue is how the c# program handles input/output.... can it take data on stdin or only filenames, etc...does it output to stdout or 2 a file, etc. The other problem is pipes on win32 can be tricky, and you may need a win32 module if using a piped method. IPC::Run uses sockets though, and is generally used on win32, so you might want to look in that direction.
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...sounds like a job for XS, SWIG or even possibly Win32::OLE.
As I've mentioned elsewhere (http://perlmonks.org/?node_id=724251), you might also want to have a look @ Dave Roths web site for Win32 stuff.
A user level that continues to overstate my experience :-))
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