From what I've heard and read, sample clearance is not an easy task and it could be costly ($1500 to $5000 per sample - for small time songs that were not hits). I use very few loops or samples aside from those that I've gotten off of legal sample CD's and of course normal drum hits.
If you are dropping an indie release, get an entertainment laywer to do the work for you. If you've been signed by a major, let them clear the samples.