Is there a program that is showing you the name of the trojans?
Or, do you already know the names of the files that need removed?
If you do not know the file names, there are diagnostic programs that give you information as to files created in the last 'x' days, files modified, etc., however, you have to figure out which files are the malicious ones, and then delete them.
If you are looking for a program that only shows the malicious files, you have to rely on AntiVirus or Malware removal programs.
Personally, I do not know of a program that identifies only malicious files.
To remove files manually, you can search for them and remove them, or you can run a 'batch' file (a text file containing a series of commands).
Retired - Doin' Dis, Dat, and slapping malware.