If so, what do I use? Emery cloth? We have used mineral spirits, brake cleaner with safe scrub sponges. I don't want to scratch it.

Before you took the pan off was it leaking? If so, you should check for distortion using a flat plate or a good machinists straight edge. (Glass is sometimes used as a flat plate.)

I worked with microwave devices for radar and to make sure the flanges were flat, they used to be "lapped" on fine sandpaper so that there were X number scratches per inch and in an even pattern.

To do this to an oil pan you would need a huge sheet of sandpaper.

For a distorted oil pan, a machine shop could true it, or perhaps a glass plate and some rubbing compound to lap it.

It was leaking a little, but the main reason we took it off was due to clogged passages. We cleaned it up pretty good, figuring better safe than sorry. Thanks for the suggestions.