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A new combined scanning electron microscope/scanning tunneling microscope SEM/STM instrument operating under UHV conditions is introduced, which allows a simultaneous characterization of morphology and surface electronic structure at variable temperatures. Moreover, by positioning the STM tip under precise control of the scanning electron microscope and using the tip as a nano-electrode spatially resolved I(V) spectra of nano-sized particles can be recorded. In the present study the morphology and electronic properties of crystalline islands of organic semiconductors have been investigated. The organic nanocrystallites have been prepared by organic molecular beam deposition of pentacene and perylene on metallic substrates and result from the pronounced dewetting occurring during growth.