The present invention relates generally to atom probes, atom probe specimens, and associated methods. For example, certain aspects are directed toward methods for analyzing a portion of a specimen that includes selecting a region of interest and moving a portion of material in a border region proximate to the region of interest so that at least a portion of the region of interest protrudes relative to at least a portion of the border region. The method further includes analyzing a portion of the region of interest. Other aspects of the invention are directed toward a method for applying photonic energy in an atom probe process by passing photonic energy through a lens system separated from a photonic device and spaced apart from the photonic device. Yet other aspects of the invention are directed toward a method for reflecting photonic energy off an outer surface of an electrode onto a specimen.