
There are audio cleaning programs like Bias SoundSoap & Roxio CDSpinDoctor (which comes with Toast) which can do this with varying degrees of success. For pops & clicks I find it is best to listen to the track with a big waveform display on your screen in an editing program. As you get to each click enlarge it so you are clearly just working on the offending sound. There are various ways to redraw the wave to remove the click. In Logic you actually get a little pencil tool. Amadeus, the Mac editor I use, has an "interpolate" feature, but even just reducing the volume of the click can work.
The problem with letting a program automatically remove all clicks is that it might think sharp percussion noises are errors too.
People making CD re-issues from vinyl use really expensive systems. It might be worth checking out mastering studios in your area that can do this professionally. Rates might be high but if you are just doing one or two sides of a 45 it will probably be less than an hour.
Finally, see if someone else has a copy that is better condition. You might be able to swap audio files with them for something else you have.
Are you going to let us know what the record is?