How to vertically and horizontally center a minipage

As your minipages are bigger than half of the page, they will need some more place on both sides of the text. Just put every two minipages in a \makebox for this. (Not my recommendation. Try to fit everything in your margins as this will look more consistent over your whole report.)

For vertical centring, just use the [p] specifier of your figure. If you use [t] instead or none at all, it will be flushed to the top if followed by text. No need for \vspace.

Load caption in order to get better spacing between captions and following images.

% arara: pdflatex \documentclass{article} \usepackage[demo]{graphicx} %\usepackage{changepage} % not needed any more \usepackage{showframe} % just for demo \usepackage{caption} \begin{document} \begin{figure}[p] \makebox[\textwidth][c]{% \begin{minipage}[b]{0.565\linewidth} \centering \includegraphics[scale=0.7]{plots/Reflex_128_Plot_xRemovals_yCPUsecondsEncoding.eps} \caption{Reflex: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_2a} \end{minipage}% \begin{minipage}[b]{0.565\linewidth} \centering \includegraphics[scale=0.7]{plots/Reflex_128_Plot_xRemovals_yCPUsecondsDecoding.eps} \caption{Reflex: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_2b} \end{minipage}}% \makebox[\textwidth][c]{% \begin{minipage}[b]{0.565\linewidth} \centering \includegraphics[scale=0.7]{plots/Lena_128_Plot_xRemovals_yCPUsecondsEncoding.eps} \caption{Lena: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_3a} \end{minipage}% \begin{minipage}[b]{0.565\linewidth} \centering \includegraphics[scale=0.7]{plots/Lena_128_Plot_xRemovals_yCPUsecondsDecoding.eps} \caption{Lena: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_3b} \end{minipage}}% \makebox[\textwidth][c]{% \begin{minipage}[b]{0.565\linewidth} \centering \includegraphics[scale=0.7]{plots/Fruits_128_Plot_xRemovals_yCPUsecondsEncoding.eps} \caption{Fruits: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_4a} \end{minipage}% \begin{minipage}[b]{0.565\linewidth} \includegraphics[scale=0.7]{plots/Fruits_128_Plot_xRemovals_yCPUsecondsDecoding.eps} \centering \caption{Fruits: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_4b} \end{minipage}}% \end{figure} \end{document} 

Another possibilities is to put pictures in table instead use minipages:

\documentclass{article} \usepackage{graphicx} \usepackage{showframe} % just for demo \usepackage{tabularx} % added package \usepackage{caption} \begin{document} \begin{figure}[p] \setlength{\tabcolsep}{2pt}% reduce space between columns in table \begin{tabularx}{\textwidth}{@{}*{2}{>{\centering\arraybackslash}X}@{}} \includegraphics[width=1\hsize]{example-image}\newline \caption{Reflex: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_2a} & \includegraphics[width=1\hsize]{example-image}\newline \caption{Reflex: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_2b} \\ \includegraphics[width=\hsize]{example-image}\newline \caption{Lena: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_3a} & \includegraphics[width=\hsize]{example-image}\newline \caption{Lena: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_3b} \\ \includegraphics[width=\hsize]{example-image}\newline \caption{Fruits: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_4a} & \includegraphics[width=\hsize]{example-image}\newline \caption{Fruits: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_4b} \end{tabularx}% \end{figure} \end{document} 

This solution require to load package tabularx, however benefits is more simple and concise code. Results is similar as show LaRiFari in his answer:

Edit: The widths of images is determined with [width=\hsize] and limited with space in cells. For enlarge this spaces reduce tabcolsep and eliminate it on beginning and end of table with @{} (see modified code).

Further reducing vertical white space with preserved aspect ratio of images is only possible with locally enlarged text width with use of \usepackage{changepage}. I do not know, if this can came to account.

You can totally get rid of the figure environment and have full control, but you will be also totally responsible for the final output. Here is an implementation with the \captionof command from the caption package that will enable you of using the largest possible space horizontally and vertically. tabularx will still be very useful.

\documentclass{article} \usepackage{graphicx} \usepackage{showframe} % just for demo \usepackage{tabularx} % added package \usepackage{caption} \begin{document} \setlength{\tabcolsep}{2pt}% reduce space between columns in table \newcommand{\HT}{4.88cm} \noindent \begin{tabularx}{\textwidth}{@{}*{2}{>{\centering\arraybackslash}X}@{}} \includegraphics[width=1\hsize,height=\HT]{example-image-A}\newline \captionof{figure}{Reflex: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_2a} & \includegraphics[width=1\hsize,height=\HT]{example-image-B}\newline \captionof{figure}{Reflex: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_2b} \\ \includegraphics[width=\hsize,height=\HT]{example-image-C}\newline \captionof{figure}{Lena: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_3a} & \includegraphics[width=\hsize,height=\HT]{example-image-A}\newline \captionof{figure}{Lena: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_3b} \\ \includegraphics[width=\hsize,height=\HT]{example-image-B}\newline \captionof{figure}{Fruits: $128 \times 128$ - Encoder} \label{plot:encoding_decoding_cpu_time_4a} & \includegraphics[width=\hsize,height=\HT]{example-image-C}\newline \captionof{figure}{Fruits: $128 \times 128$ - Decoder} \label{plot:encoding_decoding_cpu_time_4b} \end{tabularx}% \end{document}