A pixel structure for a flat panel detector is constructed in which the diode silicon and the FET silicon are simultaneously etched to form isolated structures (array photodiodes, I/O elements, and so on) in which the edges or perimeters of the diode silicon features are self-aligned to the underlying FET SI features. The full, as-deposited, thickness of the FET gate dielectric and (at least) part of the FET silicon layer remains underneath the diode silicon across the entirety of the flat panel detector.