Methods and systems for imaging and cutting semiconductor wafers and other microelectronic device substrates are disclosed herein. In one embodiment, a system for singulating microelectronic devices from a substrate includes an X-ray imaging system having an X-ray source spaced apart from an X-ray detector. The X-ray source can emit a beam of X-rays through the substrate and onto the X-ray detector, and X-ray detector can generate an X-ray image of at least a portion of the substrate. A method in accordance with another embodiment includes detecting spacing information for irregularly spaced dies of a semiconductor workpiece. The method can further include automatically controlling a process for singulating the dies of the semiconductor workpiece, based at least in part on the spacing information. For example, individual dies can be singulated from a workpiece via non-straight line cuts and/or multiple cutter passes.