This paper presents a comparative study on the effects of the in-situ surface modifications performed on “H” type microfluidic systems obtained via additive manufacturing. The microsystem was printed using a polylactic acid filament on an Ender-5 Pro printer. The surface modification of the main channel was done using chloroform by two different methods: vapor smoothing and flushing. The obtained surface roughness was studied using an optical microscope and the ImageJ software, as well as scanning electron microscopy. The effect of the channel surface treatment upon the characteristics of the fluid flow was assessed. The microfluidic systems were used for the dynamic study of biofilm growth of Candida albicans (ATCC 10231). The influence of the surface roughness of the main channel on the formation and growth of the biofilm was studied using quantitative methods, scanning electron microscopy imaging as well as optical coherence tomography.