The high-$T_c$ superconducting phase, $YBa_2Cu_3O_x$, was deposited on the single crystal MgO substrate, using a liquid aerosol feed method in a plasma enhanced chemical vapor deposition(PECVD) reactor. The effect of the plasma distribution depending on the design of a reactor was studied by the analysis of the microstructures of thin films. The particles landed were frequently observed on the films and the two causes that were responsible for the particle deposition were explained. The particles were deposited by the unstable and non-uniform plasma and the low evaporation rate of the precursors. Also, the thin film deposition rate decreased significantly as the distance between the evaporating location and the substrate increased.