In this paper we analyze the influence of source/drain (S/D) extension region design for minimizing short channel effects (SCEs) in 25 nm gate length single and double gate Silicon-on-Insulator (SOI) and Germanium-on-Insulator (GOI) MOSFETs. A design methodology, by evaluatingm the ratio of the effective channel length to the natural length for the different devices (single or double gate FETs) and technology (SOI or GOI), is proposed to minimize short channel effects (SCEs). The optimization of non-overlapped gate-source/drain i.e. underlap channel architecture is extremely useful to limit the degradation in SCEs caused by the high permittivity channel materials like Germanium as compared to that exhibited in Silicon based devices. Subthreshold slope and Drain Induced Barrier Lowering results show that steeper S/D gradients along with wider spacer regions are needed to suppress SCEs in GOI single/double gate devices as compared to Silicon based MOSFETs. A design criterion is developed to evaluate the minimum spacer width associated with underlap channel design to limit SCEs in SOI/GOI MOSFETs.