generally surface treatments are performed in solvent media. but to get exposure to only one surface, vapour treatment can be the best solution. silanes are hazardous. so looking for what is the exact protocol to perform this step.
Possibly you've already found this link http://www.microchemicals.com/technical_information/substrate_cleaning_adhesion_photoresist.pdf which is a brief explanation how to use HMDS. However, in our lab we've got a YES vacuum oven which has the HMDS bubbler integrated and a pre-set programme for treatment of Si surfaces to improve photoresist adhesion. Very safe to use.