The present disclosure relates to a MEMS package having a cap substrate with different trench depths, and a method of fabricating the MEMS package. In some embodiments, a first trench in a first device 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, with the hard mask in place, an etch is performed to the cap substrate such that an uncovered portion of a bottom surface of the first trench is recessed while a covered portion of the bottom surface of the first trench is non-altered to form a stopper within the first trench. Then, the front side of the cap substrate is bonded to a device substrate, enclosing the first trench over a first MEMS device.