Apparatus and methods are provided for enabling wafer-scale encapsulation of microelectromechanical (MEM) devices (e.g., resonators, filters) to protect the MEMs from the ambient and to provide either a controlled ambient or a reduced pressure. In particular, methods for wafer-scale encapsulation of MEM devices are provided, which enable encapsulation of MEM devices under desired ambient conditions that are not determined by the deposition conditions of a sealing process in which MEM release via holes are sealed or pinched-off, and which prevent sealing material from being inadvertently deposited on the MEM device during the sealing process.