Unfortunstely most cars have these little dents and unless you want to weld on a new roof, filler is the only solution.

First off, buff the dent right back to the metal with rough sand paper, thus giving the filler something to stick to, then once applied (leaving a little too much filler on the dent) sand it back with fine sand paper and then when nearing completion, with some wet and dry (very very very fine sand paper dipped in Warm Soapy water) The key here is to keep the roof soaking wet with said soapy water to leave the finish as smooth as possible. Dont worry if its not 100% but point it out to your body man pre-spray and he'll sort it.