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.