If your program is a console application using standard c functions, then you should be able to compile and run it in windows without altering the program first. Another option is to install Cygwin on your windows machine and recompile the program in gcc there.
You might consider writing scripts instead of compiling a C program if you want an application to run in both windows and linux, using TCL, perl, python or others.
If you want to write cross-platform gui applications, you might consider Tcl/Tk or WxWidgets:
I supplied a link for you if you are interested, however if you do a search, you may have it on your installation disk, and just need to install it.