I recently found out that the previous AP mgr at my company did not file a 1099 on a person we paid in 2001 - 2004. Do I even need to file a 1099 on him now? If yes, what do I need to do? Will I have to file a 1099 separately for each year?

Thanks! ;)

Yes, you DO have to file a separate Form 1099 for each year in question.

Your company probably will be fined by the IRS for the late filing. How much, I am not sure? Might be as much as $50 per year for every year late, plus interest.

You also need to send copies of each Form 1099 to the STATE tax authority in question, PLUS a copy to the person who did the work.