We will discuss Witten’s gauge theory approach to Jones polynomial by counting solutions to the Kapustin-Witten (KW) equations with singular boundary conditions over 4-manifolds. We will give a classification of solutions to the KW equations over $S^1\times\Sigma\times R^+$. We prove that all solutions to the KW equations over $S^1\times\Sigma\times R^+$ are $S^1$ direction invariant and we give a classification of the KW monopole over $\Sigma\times R^+$ based on the Hermitian-Yang-Mills type structure of KW monopole equation. This is based on joint works with Rafe Mazzeo.