Yes. The Arduino is programmed in C/C++ using a standard C++ compiler (gcc). You can use any standard constructs. For your convenience there are Arduino libraries provided to encapsulate some of the features of the Amtel hardware but you don't have to use them. The IDE hides a little of this from you in that you don't provide main(), it does, and provides setup and loop instead to make the initial learning curve a bit less steep. You don't have to use the IDE either.