\documentclass{article}
\usepackage{graphicx}
\usepackage{amssymb}
\usepackage{epstopdf}
\usepackage{multicol}
\usepackage{subfigure}
\begin{document}

\section{multicol} 
Figure~\ref{Noise:ENC1} and Figure~\ref{Noise:ENC2} .

\begin{figure}[hptb]
\begin{multicols}{2}
\begin{center}
\includegraphics[width=0.49\textwidth]{figures/fig1.eps}
\end{center}
\caption{Caption of figure 1.}
\label{Noise:ENC1}
\begin{center}
\includegraphics[width=0.49\textwidth]{figures/fig2.eps}
\end{center}


\caption{Caption of figure 2.}
\label{Noise:ENC2}
\end{multicols}
\end{figure}

\section{subfigure} 

\begin{figure}[ht!]
\centering
\subfigure[]{\includegraphics[width=0.49\textwidth]{figures/fig1.eps}}
\subfigure[]{\includegraphics[width=0.49\textwidth]{figures/fig2.eps}}
\caption{Length deviation of the SCT
      barrel flange interferometers: (a) 24hr stability before
      cooling stoppage and (b) during a cycle of the ATLAS
      solenoid.}
\end{figure}


\section{simply include twice} 

\begin{figure}[ht!]
\centering
\includegraphics[width=0.48\textwidth]{figures/fig1.eps}
\includegraphics[width=0.48\textwidth]{figures/fig2.eps}
\caption{\label{fig:GLI}{\emph{The Grid Line Interferometer design for
      the ATLAS FSI system. The wide angle beam emerging from the
        EC.}}}}
\end{figure}

\end{document}