We have investigated the shapes, thickness, density, composition, and quality of Ge/Si(001) islands grown by solid source molecular beam epitaxy in ultra high vacuum conditions. Nano crystals were formed by means of the Stranski-Krastanow “self assembly” growth mechanism. 5 nm of Ge were deposited on Si(001) substrates, at 500 °C, with deposition rate of 0.5 nm/min. Atomic force microscope measurements reveal islands of various sizes, ranging from 60 nm to 700 nm in diameter. Islands' density found to be correlated with their sizes, with denser areas containing mostly islands of the smaller sizes. Micro Raman spectroscopy, with probing spot of about 0.7 µm diameter, has been used to study the composition, thickness and crystalline quality of the islands. Data were taken at various points on the sample distinguishing between various islands' types. Combined analysis of Raman spectra and the micrographs reveal low amount of alloying (less than 30%) in all types of islands, with the larger islands showing the more amount of intermixing. High crystalline quality of the layers within the islands suggests negligible amount of dislocations.