If you have the bismark tip, then yes, but be careful how much you squeeze in or you'll break the cupcake.
Your other option is to use something like an apple corer and take out a center core and fill that. Some will put a bit of that removed core in for the top, before icing. But I'd just ice right over top. If you watch Cupcake Wars you'll see that most of them use the center core and just fill and ice.
I stick my finger smack down the center. With clean fingers, of course!
I insert a large star tip and squeeze in some filling until it *feels* right...unless it is a really thick filling (like homemade caramel) then I use a paring knife to cut out a little core and fill it that way.
I use the tool that is originally for shaping melon balls. Works great with cupcakes, too 
. You can either cut of the "cap" and put it back on the Cupcake after filling or simply ice over as already mentioned.
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