Are you looking at the actual subfloor? As in plywood or tongue and groove boards? Or is it the finished floor? Tile, lino, or hardwood?
It's normal for the finished floor to run under the dishwasher. But if the cabinets weren't raised 3/4" when they were installed it creates problems.
Did you recently replace your counter tops?
Did you have problems getting the old one out?
Your easiest solution might be to call your appliance dealer and explain your problem. Ask if there is a shorter model.
I would look at removing the finished floor surface from under the dishwasher before I would tear up counter tops.