Non-invasive characterization and quantitative analysis of embedded microstructures are essential aspects when dealing with microfluidic platforms. This relevance is even more evident in micro-channels embedded in fused silica quartz, fabricated by laser-assisted-etching in HF solution. For these structures, an optimal optical imaging requires extremely flat and smooth surfaces as to avoid cylindrical lens effect and light scattering. The typical internal walls roughness left by laser micromachining is a critical aspect to be taken into account when dealing with on-chip imaging. In this work we investigate the internal walls roughness through a micro-cavity scanning tomography system, able to acquire quantitative optical measurements directly in close embedded micro channels, and so in a non-invasive way. This system combines the advantages of a low-coherence system with a lens-free configuration and high sensitivity of the optical cavity, suitable for metrology of lab-on-a-chip internal structures. (C) 2016 Elsevier B.V. All rights reserved.