For my IDL and MATLAB scripts, calling scp is as easy as using each language's system call, with command strings built up through normal concatination.
IDL:
In IDL it's the "spawn" command. Here are some nice tutorials with examples:
http://archive.stsci.edu/iue/manual/dacguide/node8.html
http://www.astro.virginia.edu/class/oconnell/astr511/idl_5.1_html/idl1a9.htm
http://idlastro.gsfc.nasa.gov/idl_html_help/SPAWN.html
MATLAB:
This shows a very fancy script, but it's just a wrapper for the system call that allows specification of an array of scenarios for the scp command. The take-away for me was to be sure to use the full path for the scp executable.
http://www.mathworks.com/matlabcentral/fileexchange/25256-scpsftp-from-matlab/content/ssh/scpfrommatlab.m
