How to cut pdf at crop marks?

The pdfcrop utility is made to crop the white borders from a PDF.

pdfcrop in.pdf out.pdf

If you want to remove a little MORE so that the crop marks are also removed, then use the --margins option. Providing a negative margin value will cause a crop of some of your content. The margin value unit is bp. Play with the negative value to remove your tick marks and nothing else.

pdfcrop --margins -10 in.pdf out.pdf 

Edit Using OP's sample PDF follows...

Your sample PDF file works for me. I used the following command.

pdfcrop --margins -10 --verbose matC.pdf matC_cropped.pdf

This is your original file

And this is the cropped file

The pdfcrop verbose log follows

PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
* PDF header: %PDF-1.5
* Running ghostscript for BoundingBox calculation ...
GPL Ghostscript 9.04 (2011-08-05)
Copyright (C) 2011 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Processing pages 1 through 1.
Page 1
%%BoundingBox: 3 3 205 205
* Page 1: 3 3 205 205
%%HiResBoundingBox: 3.667289 3.061336 204.622728 204.016705
* Running pdfTeX ...
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (MiKTeX 2.9 64-bit)
entering extended mode
(tmp-pdfcrop-3248.tex [1 <./matC.pdf>] )
Output written on tmp-pdfcrop-3248.pdf (1 page, 24335 bytes).
Transcript written on tmp-pdfcrop-3248.log.
==> 1 page written on `matC_cropped.pdf'.

As you see, pdfcrop used ghostscript. Perhaps your ghostscript has an issue.

I finally solved the problem using the option fitpaper=true (manually setting the trim option).

\documentclass{article}
\usepackage{pdfpages}
\begin{document}
\includepdf[pages={2-32},trim=2.9cm 3.5cm 2.9cm 3.5cm,fitpaper=true]{Chapter05.pdf}            
\end{document}

EDIT: If I think to non LaTeX solutions, briss comes up to my mind.