We have studied direct bonding and thinning of pre-etched silicon wafers. Silicon-on-insulator (SOI) substrates with pre-etched cavities provide freedom to MEMS design and enable manufacturing of advanced sensor structures (sensor structures that would be difficult or impossible with conventional substrates). Cavities with different shapes and sizes were etched on to the handle wafers. The etched handle wafers were bonded to unpatterned cap wafers in air or in vacuum. The bonding quality was evaluated with scanning acoustic microscopy and with HF-etching test. After bonding, the cap wafers were thinned down with grinding and polishing. The thickness variation of silicon diaphragm over the cavities was evaluated with cross-sectional SEM. The deflection of the Si film was measured with surface profilometry. To decrease the deflection and the thickness variation of the film, different support structures were placed inside the cavities.The bonding experiments carried out with patterned wafers showed that vacuum bonding results in slightly higher bonding energy than bonding in air. With large cavity fraction (80% of total wafer area), the air bonded samples had large void on the bonded interface. With smaller cavity fractions or with vacuum bonded samples, no such voids were found. Thinning studies showed that the thickness variation of the silicon diaphragm increases with increasing cavity dimensions and with decreasing SOI layer thickness. Thickness variation can be reduced with support structures under the Si membrane.