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I have batch of files named A-01.pdf, A-02.pdf, B-01.pdf, B-02.pdf.... Then I have folder structure 01, 02, 03,.... How can I move all the files with 01 in there name to folder 01, all with 02 to folder 02 and so on?

There are a lot of scripts on the net but none of them seams to fit my case.

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Assuming that these files are all in the same folder and the numbered folders are part of that folder as well, open Terminal and run

cd path/to/folder
for i in *.pdf; do
    mv "$i" "${i:2:2}/"
done
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A script like @patrix's is probably the most efficient way, but if you're not comfortable with running shell scripts, you could do it with Automator, with a workflow that looked something like this:

First steps of potential workflow

and so on for -03, -04 etc. (There's probably an even more efficient way to do it with Automator using loops and variables, but I've never tried using those...)

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