An atmospheric-pressure microplasma jet operating in helium gas has been used in a side-on configuration to modify locally the surface energy of polystyrene (PS). The plasma plume and gas outflow emanating from the capillary-type discharge (8 kVp–p at 30 kHz excitation) were directed parallel to (side-on) and just above the sample surface, rather than head-on as in conventional treatment. This side-on treatment method has been shown to prevent surface damages, pitting or roughing caused by head-on treatment methods. Schlieren photography has been used to identify regions of laminar and turbulent flow in the exiting gas stream and the nature of their interaction with the substrate surface. Correlation of these observations with spatially resolved water contact angle (WCA) measurements of the treated PS, show clearly that substantial reductions in WCA (∼50–60°) occur in downstream regions where the turbulent gas mixed with air impinges the surface. In contrast, only small changes in WCA occur (∼10–20°) in regions closer to the exit orifice where the helium (He) flow is still laminar across the surface. Little or no treatment is observed for distances greater than 5 cm from the source. In addition, low levels of treatment were observed in the regions where the visible plasma glow of the jet is adjacent and parallel to the surface. The results indicate that excited air species (either mixed or entrained in the He gas flow) are the main agents causing surface covalent bond breaking leading to surface modification.