System and method for nanoscale X-ray imaging. The imaging system comprises an electron source configured to generate an electron beam along a first direction; an X-ray source comprising a thin film anode configured to receive the electron beam at an electron beam spot on the thin film anode, and to emit an X-ray beam substantially along the first direction from a portion of the thin film anode proximate the electron beam spot, such that the X-ray beam passes through the sample specimen. The imaging apparatus further comprises an X-ray detector configured to receive the X-ray beam that passes through the sample specimen. Some embodiments are directed to an electron source that is an electron column of a scanning electron microscope (SEM) and is configured to focus the electron beam at the electron beam spot.