We're using Raspberry Pi 3's as prototypes but don't need the USB ports, as well as some of the other ports. Are they easily removable?

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Yes, you can remove some or all of the USB ports, and/or the Ethernet jack if required. Adafruit has a guide on reducing the USB and Ethernet ports. Node's taken it even farther. There's more to it than can reasonably be summarized here, unfortunately.

You might also look at other boards. There are slimmer quad core boards available from NanoPi, Orange Pi and others if you just need a basic board.

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