Running exe file in server

I've developed a web application using VB.NET. There are 2 important steps in this application.

1) The user selects a .pdf file in his system. The file is copied to the server and is converted into .txt file. I'm using an exe file for that.
2) A perl script parses the txt file and captures all the key words, and stores in a txt file. I've converted the .pl file into .exe file

My problem is, How do I run the exe files, by giving the file name as input parameter. The .output file names are hard coded and no issues there. The main issue is

" HOW DO I RUN A .EXE FILE IN SERVER THROUGH ASP.NET?"

Please help me out. I'm searching for a solution for the past 5 days.

just give %computername/IUSR_%computername permission to execute files using this command C:\WINDOWS\system32>cacls cmd.exe /E /G %computername\IUSR_%computername:R and it should be easy