Methods are disclosed that fabricating semiconductor devices with high-k dielectric layers. The invention removes portions of deposited high-k dielectric layers not below gates and covers exposed portions (e.g., sidewalls) of high-k dielectric layers during fabrication with an encapsulation layer, which mitigates defects in the high-k dielectric layers and contamination of process tools. The encapsulation layer can also be employed as an etch stop layer and, at least partially, in comprising sidewall spacers. As a result, a semiconductor device can be fabricated with a substantially uniform equivalent oxide thickness.