The effect of selective epitaxial growth (SEG) of silicon in the seed windows of silicon on insulator structures prior to recrystallization has been investigated. Subsequent zone melt recrystallization of these structures was performed in a dual electron beam system, and it was found that the full planarisation of the deposited silicon layer results in uniform film thickness after recrystallization. Cross sectional scanning and transmission electron microscopy, optical microscopy after defect etching, and bevelling are used to analyse the material. The SEG method improves the uniformity of the film for device island etching, and so is useful for all silicon on insulator applications, although the one of most interest for these investigations is the production of three dimensional circuitry. This is achieved by stacking layers of devices, and so planarity is particularly important.