TS interaction with Windows dialog?

System

Is there anything native to or easily integrated with TeamSite that is able to interact with a Windows dialog?

For instance, there is a tool that I would like to use as part of an external task. This tool essentially converts a file to a different format, but (at the moment) prompts for a filename to save the converted file. I'm investigating to see whether we can do all of this stuff on command line, as this is the greatly preferred method, but I'm wondering if anyone has had this problem before and how they've handled it.

Dave

Current Environment(s):
(1) TS 6.5 on W2K3
(2) TS 6.1 SP1 on W2K3
By the way, I miss Unix terribly.