This paper presents a new and innovative process of modification of wetting of open micro-channels involving a method to seal the microfluidic devices. Allylamine was polymerized on poly(dimethylsiloxane) (PDMS) by plasma-enhanced chemical vapour deposition (PECVD) to modify the wetting properties of open micro-channels. The sealing of the devices was done by thermal pressing. All the steps of the process were characterized by different analysis techniques to understand the mechanisms of the process and to assess the performance of the technique. Physicochemical analysis of the polymerized allylamine coatings (X-ray photoelectron spectroscopy and static water contact angle) showed that the coatings were resistant to the thermal pressing and were stable in ambient air and underwater up to 14 days of ageing, even if the water contact angle decreased during the underwater ageing. Parallel tests were undergone in microfluidic devices and the stability of ageing was tested by the production of the simple oil-in-water emulsions. All the experiments showed that this new PECVD/thermal press process is an effective way to modify the wetting properties of an open microfluidic device and includes a technique to seal effectively the system afterwards.