A semiconductor device having multiple fin heights is provided. Multiple fin heights are provided by using multiple masks to recess a dielectric layer within a trench formed in a substrate. In another embodiment, an implant mold or e-beam lithography are utilized to form a pattern of trenches in a photoresist material. Subsequent etching steps form corresponding trenches in the underlying substrate. In yet another embodiment, multiple masking layers are used to etch trenches of different heights separately. A dielectric region may be formed along the bottom of the trenches to isolate the fins by performing an ion implant and a subsequent anneal.