A comparative study of the structural, microstructural and magnetic properties of CrO$_2$ thin films grown onto (110) and (100) TiO$_2$ rutile single crystal substrates by chemical vapor deposition (CVD), using CrO$_3$ as chromium precursor and either oxygen or argon as carrier gas is presented. Our results show that growth under argon carrier gas leads to high quality CrO$_2$ epilayers with structural and magnetic properties similar to those obtained using the more standard oxygen carrier gas. Furthermore, we interpret the larger magnetic coercivity observed for the (110) oriented films in terms of their microstructure, in particular of the highest strain and edge roughness of the building structures of the CrO$_2$ epilayers, which are settled by the substrate crystallographic orientation. ; Comment: 27 pages, 2 tables, 8 figures