Are they welded to a deck? Flat surface on top of the structure...or are they attached to the hull itself?  

As long as what your removing is welded to a deck surface only....you can grind the welds down and bust them loose.  You will more than likely end up with some holes in the deck that need to be welded or patched.   If this stuff is attached to the ribs or hull of the boat then you will need a gtaw (tig) welder and somone who can use it well.  Most of any interior structure is welded down using mig but you will want to Tig any spot repairs.  Any damage to the ribs or hull will have to be reparied properly or you will likely have cracks start to form and problems later on.  Aluminum boats flex quite a bit during use so holes or tears in the wrong places tend to grow.   I built these things for about 5 years so if you have any other questions I will try to help.