The present invention relates to a method of fabricating a microfluidic device including at least two substrates provided with a fluid channel, comprising the steps of: a) etching at least a channel and one or more fluid ports in a first and/or a second substrate; b) depositing a first layer on a surface of the second substrate; c) partially removing the first layer in accordance with a predefined geometry; d) depositing a second layer on top of the first layer and the substrate surface; e) planarizing the second layer so as to smooth the upper surface thereof; f) aligning the first and second substrate; g) bonding the first substrate on the planarized second layer of the second substrate.