The present invention provides an improved amorphization/templated recrystallization (ATR) method for fabricating low-defect-density hybrid orientation substrates. ATR methods for hybrid orientation substrate fabrication generally start with a Si layer having a first orientation bonded to a second Si layer or substrate having a second orientation. Selected regions of the first Si layer are amorphized and then recrystallized into the orientation of the second Si layer by using the second Si layer as a template. The process flow of the present invention solves two major difficulties not disclosed by prior art ATR methods: the creation of “corner defects” at the edges of amorphized Si regions bounded by trenches, and undesired orientation changes during a high temperature post-recrystallization defect-removal annealing of non-ATR'd regions not bounded by trenches. In particular, this invention provides a process flow comprising the steps of (i) amorphization and low-temperature recrystallization performed in substrate regions free of trenches, (ii) formation of trench isolation regions that subsume the defective regions at the edge of the ATR'd regions, and (iii) a high-temperature defect-removal anneal performed with the trench isolation regions in place.