ouch! I deserve all the criticism, this was probably my worst node. I was reading everything and I couldn't make sens out of it so I wrote something that kind of made sens to me. Anyways, I just started learning Perl so you guys have to give me some credit :)
Back to the program, the file.exe opens up like command prompt and in the folder where file.exe is, there is an input file "base.in". So, I need to open file.exe through perl and type in "base" in file.exe for it to take the input file and run. The input file is created by the Perl program. Instead of taking the input file and passing it to file.exe, I'm trying to pass it through the perl program. After running, the program outputs text files into the folder. I would need to read the text file on Perl as well but I guess that's for another time ;).