No (at least not at the moment).
TrIDScan expect that all the files you want to analyze are in the same folder.
By the way, I basically cannot use a Win PC before I install the
Total Commander file manager. With it, it's just trivial to locate all the interesting files (for example, all the *.JS files under the folder "\windows" & subfolders and copy them in a "\temp" one. Since I'm totally adept at using it, I personally havent ever expericed the need of recursive scanning.
Bye!