I would suggest you take a look at PDFcrop.

If you wish to crop a pdf with left, top, right and bottom margins of 5, 10, 20, and 30 pt (points), then run

pdfcrop --margins '5 10 20 30' input.pdf output.pdf

in terminal. To actually crop something away, use negative values in the argument for crop. For example,

pdfcrop --margins '-50 -50 -50 -50' input.pdf output.pdf

crops 50 pts from the left, top, right, bottom (in this order).

If you run only the command pdfcrop input, it will output a file titled input-crop.pdf with zero margins. I find this very handy when including pdf illustrations in documents.

Cropping multiple files

Unfortunately, pdfcrop cannot crop multiple files at the time. It is however easy to write a script that will crop all pdfs in the folder the script is located in.

Create a new empty file, and call it something.sh. Open it with a text editor and insert the following:

#!/bin/bash

for FILE in ./*.pdf; do

  pdfcrop "${FILE}"

done

Save it, and close. Then right click the file, go to Properties > Permissions and check the field Allow executing file as program. Now close the dialog. Run the script by double clicking it and choosing Run in Terminal. And new, zero-margin cropped version of all pdfs with suffix -crop will now be printed in the folder. If you want margins or other things, you can of course just open the script and add arguments after pdfcrop.