Next code shows a possible solution which uses absolute coordinates (current page) to cover certain region.
Another solution could be to include tikzmarks in your text and use them to draw covered regions.
\documentclass{beamer}
\usepackage{tikz}
\usepackage{lmodern}
\begin{document}
\begin{frame}
\begin{columns}[onlytextwidth]
\column{.5\linewidth}
\begin{itemize}
\item First
\item Second
\item Third
\end{itemize}
\column{.5\linewidth}
\begin{figure}
\includegraphics[width=.9\textwidth]{example-image}
\caption{A nice figure}
\end{figure}
\end{columns}
\tikz[overlay, remember picture] \fill[red, opacity=.3] ([shift={(1cm,1cm)}]current page.south west) rectangle ++(6cm,4cm);
\tikz[overlay, remember picture] \fill[green, opacity=.3] ([shift={(-1cm,-1cm)}]current page.north east) rectangle ++(-2cm,-7cm);
\end{frame}
\end{document}
