Material Extrusion (MEX) is an Additive Manufacturing technology widely used for the fabrication of polymeric, metallic and composite parts with clear advantages. In the last decades, the growing interest of such industries like aerospace, medical, automotive and R&D has driven technological improvements of MEX to make the technology more reliable and repeatable. Although, defects and geometric dimensional inaccuracies are still known to affect the process, limiting the applicability of MEX for the realization of functional parts. Recently, in-process monitoring methods have been implemented for a rapid detection of defects and process anomalies, activating, eventually, the control of the process. In this work, an innovative layerwise monitoring methodology based on a high-resolution blue laser line profilometer applied to a MEX process, was proposed. By analyzing the point clouds of each layer, with proper quality indexes, it was possible to compute the layer height deviation and to evaluate the surface quality in terms of occurrence of defects. In particular, the quality indexes presented in this work were representative of the layer height accuracy, the occurrence and distribution of defects on the layer surface and the stability of the process (respectively the so-called indexes were ADLH, RAD and the slope s). Different process conditions were generated by varying the raster angle and the sample location on the building platform.