When generating STL files with slic3r I would like to automatically prefix the filename with strings such as PLA or PET before uploading to my printer. How can I specify this in the filament settings?
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The filename is under the "Print settings" tab. Under output options, you can change the name template. You can use words like: [layer_height] to make the name dynamic.
The variable you are looking for here is: [filament_preset] But the full name, with space and everything, is used.
Here is a link to fuller docs: https://github.com/slic3r/Slic3r/wiki/FAQ#how-can-i-specify-a-custom-filename-format-for-output-g-code-files
New version of Slic3r
It lets you edit the filename when upload it. You will see what will be upload it and give it any name. But this is a manual process. Just updated my answer for the sake of completeness.

Gunslinger
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2Very useful answer. The reference to the slic3r doc is helpful, and explains a lot about variable substitutions. I need to find the canonical list of variables, just for reference. Thank you. – cmm Jul 01 '18 at 16:37
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Verified and working perfectly for me. Thanks! – Mark Harrison Jul 02 '18 at 21:59