Some clarity still missing for me (YMMV)

1. After selecting the file from dropdown box in CGI page,
2. i have to insert some text in that selected pdf file for that i am using exe.
3. After that i need to upload the edited pdf file.
    
4. So, I need to execute program at server side.

So, despite OP's final statement, I don't think this unambiguously means modification of the .pdf on the server side.

Line by line:

1. Probably means server side...unless "dropdown" really refers to a upload-selection-box (ie: user at client selecting a file from the client machine).
2. Appears to mean OP is using a Windows .exe to modify the .pdf: At the client or at the server NOT determined as server could be running on 'doze.
3. Use of "upload" instead of "save" or "e;write" suggests transmission from the client to the server

   in which case

4. execution of the .exe may be anticipated on the client side.

That would be "a whole 'nuther case," so, I seek clarification.