What is the best way to prep a concrete floor that had ceramic tile before, I removed it with a chipping gun and tried to skim all the high spots, but after the dust settled I notice that there are still high spots and low spots. Not to concerned about low spots because they can be filled in with thin set.

Your low spots must all be brought up to the level of your high spots. Unless you have a small isolated spot that is high you need to forget chipping and go with a self leveling cement. I would also recommend that you not tile directly on the cement floor, cracking will likely happen. Do some research on Ditra Schluter-DITRA - Schluter-Systems so you can eliminate this problem.

1 wanted to say thank you for your help. Sorry I didn't get to you before now but as you are probably aware of a bathroom remodel is a lot of work and one thing after another. All is going well. Do you know of any helpful tips for grouting, especially the final clean up. I know about using plenty of clean water, 3 bozo buckets works fairly well.
Hope this is the right way to thank you.