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We studied laser-microdissection of standard and Langmuir-Blodgett (LB) nanotemplate protein crystals in glycerol solution. The time required for microdissection was significantly longer for LB-crystals as compared to standardcrystals which also more rapidly dissolve. Microfragmentation of lysozyme crystals was observed after extended solvent exposure. Synchrotron radiation nanobeam mapping allowed localizing and aligning cryofrozen lysozyme microfragments. 3D data-sets obtained from two microfragments were refined to atomic resolution. The well-defined electron density maps showed no evidence for damage of radiation of sensitive side-groups. Our results suggest applications of laser-microdissection techniques in structural studies on crystals with a high mosaicity. They also provide a new window for the characterization of protein crystal organization down to the submicron scale, pointing to a new emerging biophysical technique.