A conventional path integral quantization of the Chern-Simons theory is performed by Alvarez Gaumé. The author applies gauge fixing, Faddeev-Popov construction and computation of the one loop effective action. The main result is the level renormalization at one loop $k\rightarrow k+c_v$ . ($c_v$ is the Coxeter number of the gauge group).
Further perturbative results were obtained by: Giavarini Martin and Ruiz Ruiz. (They use a different regularization scheme by adding a Yang-Mills term and taking the large topological mass limit). They show that the level renormalization does not change at the two-loop level and compute the Wilson loop expectation value.
Nonperturbative results of the Chern-Simons theory can better be obtained by means of canonical quantization. In many cases the gauge redundancy can be removed exactly and only a finite number of degrees of freedom are left, which can in tern be canonically quantized. Please see for example the following review by Dunne (section 3), where the quantization in the case when the space time manifold is $T^2 \times \mathbb{R}$ is performed.