The present disclosure describes methods for transferring a desired layout into a target layer on a semiconductor substrate. An embodiment of the methods includes forming a first desired layout feature as a first line over the target layer; forming a spacer around the first line; depositing a spacer-surrounding material layer; removing the spacer to form a fosse pattern trench surrounding the first line; and transferring the fosse pattern trench into the target layer to form a fosse feature trench in the target layer, wherein the fosse feature trench surrounds a first portion of the target layer that is underneath a protection layer. In some embodiments, the method further includes patterning a second desired layout feature of the desired layout into the target layer wherein the fosse feature trench and the protection layer serve to self-align the second desired layout feature with the first portion of the target layer.