The present disclosure relates to a MEMS package having different trench depths, and a method of fabricating the MEMS package. In some embodiments, a first trench in a first device region, a second trench in a second region, and a scribe trench in a scribe line region are formed at a front side of a cap substrate. Then, a hard mask is formed and patterned over the cap substrate. Then, a stopper is formed by performing an etch to the cap substrate such that a first portion of a bottom surface of the first trench uncovered by the hard mask is recessed while a second portion of the bottom surface of the first trench covered by the hard mask is non-altered to form a stopper within the first trench. Then, a second etch is performed to the second trench to lower the bottom surface of the second trench.