Nanowire formation in Si-based polymer thin films using a heavy ion beam is discussed in terms of energy density deposition along ion tracks. Gelation of the polymer along the ion track results in cross-linking to produce nanowires with size and number density controllable by selecting appropriate ion beam characteristics and polymer materials. Ion bombardment of poly(carbosilane) (PCS), PCS-poly(vinylsilane) blend polymer, and poly(methylphenylsilane) produces nanowires with radii of 7-30 nm depending on the type of ion beam. The difference in size is shown to be related to the efficiency of the cross-linking reaction considering the deposited energy distribution along the ion tracks.