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I want apply a Macro created in N++ to multiple files stored in a folder or multiple folders.

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What is your macro doing? How many files? Do you need it to work for a long period of time or will the macro change over time/depending on the file? I've been in a similar situation, then I learned python and it solved everything. This is something that seems like it would be easily programmable but might be more involving using just notepad++. Give me any extra details and maybe I can help. I'd be willing to write the code for you depending on what you wanna do. – BiTinerary Jun 20 '15 at 3:26

You can end your macro by saving your document (Ctrl+S) and closing the window (Ctrl+W).

Or if you don't want the document to be closed, you can end the macro by changing the tab (Ctrl+Tab).

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