A novel method for patterning optically active colloidal PbSe nanocrystals on Si surfaces is reported. Oleate-capped PbSe nanocrystals were found to adhere preferentially to H-terminated Si surfaces over oxide and alkyl-terminated Si surfaces. Scanning probe lithography was used to oxidize locally a dodecyl monolayer on the Si surface of a silicon-on-insulator wafer prepatterned with photonic crystal microcavities. Aqueous HF was then used to remove the oxide and expose H-terminated Si areas, yielding patterned PbSe nanocrystals on the Si surface after exposure to a nanocrystal solution. This patterning technique allows for the selective deposition of PbSe nanocrystals at the main antinode of the silicon-based microcavities. More than a 10-fold photoluminescence enhancement due to the cavity-nanocrystal coupling was observed.