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I often have to copy-paste files from 2 finder folders. I use the cmd + ` shortcut. But it cycles through Window 1 > Desktop > Window 2.

Is there a way to skip desktop?

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Desktop is a folder, so cycling between active folder is an expected behavior in Finder. The only way to achieve what you want is to hide Desktop by entering the command below.

defaults write CreateDesktop FALSE

After this, cycling between window will happen to the folder you’ve opened. This suggestion is recommended only if you don’t use Desktop to place temporary files.

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I use my desktop for temporary files, so I guess I won't be able to use it. – Pritesh Desai Apr 16 '14 at 18:46
How about trying Unclutter for Mac to place temporary files. This way you can maintain a clean desktop, while cycling between window smoothly. :) – sayzlim Apr 16 '14 at 18:49
Completely forgot about CreateDesktop — oops :) – grgarside Apr 16 '14 at 18:49

If your goal is to go back and forth between two windows several times in a row, you can alternate between ` and `, which goes the other way round.

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Yes, it does work but hitting cmd+' twice is quicker than using shift. <Being Lazy> – Pritesh Desai Apr 17 '14 at 3:10

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