\documentclass{article}
\usepackage[demo]{graphicx} % "demo" option just for this example
\usepackage{subcaption}
\begin{document}
\begin{figure}[t!] % "[t!]" placement specifier just for this example
\begin{subfigure}{0.48\textwidth}
\includegraphics[width=\linewidth]{pic1.pdf}
\caption{First subfigure} \label{fig:a}
\end{subfigure}\hspace*{\fill}
\begin{subfigure}{0.48\textwidth}
\includegraphics[width=\linewidth]{pic2.pdf}
\caption{Second subfigure} \label{fig:b}
\end{subfigure}
\medskip
\begin{subfigure}{0.48\textwidth}
\includegraphics[width=\linewidth]{pic3.pdf}
\caption{Third subfigure} \label{fig:c}
\end{subfigure}\hspace*{\fill}
\begin{subfigure}{0.48\textwidth}
\includegraphics[width=\linewidth]{pic4.pdf}
\caption{Fourth subfigure} \label{fig:d}
\end{subfigure}
\medskip
\begin{subfigure}{0.48\textwidth}
\includegraphics[width=\linewidth]{pic5.pdf}
\caption{Fifth subfigure} \label{fig:e}
\end{subfigure}\hspace*{\fill}
\begin{subfigure}{0.48\textwidth}
\includegraphics[width=\linewidth]{pic6.pdf}
\caption{Sixth subfigure} \label{fig:f}
\end{subfigure}
\caption{My complicated figure} \label{fig:1}
\end{figure}
A cross-reference to Figure~\ref{fig:1}, and a cross-reference to Subfigure~\ref{fig:e}.
\end{document}