Possible to suppress popups?

Is it possible to suppress popups when using CreateProcess to launch another application. I have a command line application that I need to run, and if it encounters a certain error, it spits out a popup. I want to run this application completely silently.

No, but you could detect it and then send a mouseclick so the popup goes away again.

Check whether the program you're running has a "silent mode" command-line option. Sometimes they will.