So I installed Ubuntu 16.04 on my laptop which as a high resolution display which worked well with scale factor 2.

Now I have connected an external monitor which requires a scale factor 1. I update this in System Settings, and some of the windows are scaled correctly (example: HexChat, Chrome, Launcher) but others are too big (Terminal, File Browser):

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How can I scale down all windows?

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I figured it out. For others with the same issue, if you want to change the scale mode on Ubuntu 16.04 (Unity), there are three places to change:

System Preferences > Screen Display > Scale for menu and title bars:

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Tweak Tool > Fonts > Scaling Factor:

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Tweak Tool > Window > Window Scaling:

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