As long as it is %99 isopropyl alcohol yes then it is fine. Some people will recommend q-tips to clean off the old thermal grease, but I prefer coffee filters.
Q-tips can leave cotton behind, something you don't want on a surface that has the potential to get very hot. Coffee filters on the other hand are very gentle and don't leave any residual material.
Acetone, (nail polish remover), also works really well too. Better then %99 isopropyl alcohol, (rubbing alcohol). Just be patient with cleaning it and take your time to do it right.