Methods for protecting gate stacks during fabrication of semiconductor devices and semiconductor devices fabricated from such methods are provided. Methods for fabricating a semiconductor device include providing a semiconductor substrate having an active region and a shallow trench isolation (STI) region. Epitaxial layer is formed on the active region to define a lateral overhang portion in a divot at the active region/STI region interface. A gate stack is formed having a first gate stack-forming layer overlying the semiconductor substrate. First gate stack-forming layer includes a non-conformal layer of metal gate-forming material which is directionally deposited to form a thinned break portion just below the lateral overhang portion. After the step of forming the gate stack, a first portion of the non-conformal layer is in the gate stack and a second portion is exposed. The thinned break portion at least partially isolates the first and second portions during subsequent etch chemistries.