Monitoring wettability properties of surfaces is a major concern in microfluidic applications and a lot of studies have been devoted to the development of surface functionalization technologies by grafting self-assembled monolayers on flat surfaces or inside microchannels using either liquid phase (polymer microchannels) or vapor phase (silicon mi- crochannels). However those processes are not fast, nor easy, nor well adapted to the treatment of a large number of pieces. In this paper, we propose a simple and low cost vapor deposition method enabling the modification of all polymer devices (polyimide, epoxy, PDMS...) and so the monitoring of microchannels network wettability. The vapor deposition was made using SPD (Surface Preparation Deposition) equipment from Memsstar using SiCl4 and H20. Water hydrolyzes silicon tetrachloride giving birth to silanol groups which react with the sample surface to form a silicon dioxide layer and therefore a hydrophilic surface. To obtain a hydrophobic surface perfluorodecyltrichlorosilane (FDTS) and water was used. Deposition was made at 40◦C and low pressure. Modified surfaces were first characterized by static water contact angle measurement: a wettability angle of 25◦ was obtained for SiO2 layer, and 110◦ for FDTS. The treatment was reproducible and stable over period of six month at least. These values have to be compared to the native contact angle of standard polymers which lies generally in the range 80◦-85◦. Microchannels were manufactured using standard PDMS soft lithography or by laminating epoxy based photoresists. Complete devices were introduced in the SPD reactor and deposition performed. Channels were 200μm wide, 20μm high and 2cm long. Deposition in microchannel was demonstrated and the uniformity of the deposited layers was evaluated by studying the capillary filling of channels with various liquids.