Where the pops there right away or did they show up after a couple of days? How big are the "pops"? and are they raised? If they are solvent pops, as 302z28 said, block sand them out and re-clear as he mentioned. The only time you would need to re-base is if you burned through in trying to get rid of the pop.
If you can answer the top three questions, I can determine exactly what they are and offer solutions.