One embodiment relates to a method of automated inspection of scattered hot spot areas on a manufactured substrate using an electron beam apparatus. A stage holding the substrate is moved along a swath path so as to move a field of view of the electron beam apparatus such that the moving field of view covers a target area on the substrate. Off-axis imaging of the hot spot areas within the moving field of view is performed. A number of hot spot areas within the moving field of view may be determined, and the speed of the stage movement may be adjusted based on the number of hot spot areas within the moving field of view. Another embodiment relates to an electron beam apparatus for inspecting scattered areas on a manufactured substrate. Other embodiments, aspects and features are also disclosed.