Does anyone know what program Phil Fish is using to edit models of levels? Or is it it something he built himself? I'm new to game development and was looking for something to design levels with besides my notebook.
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"Bedard and Fish created their own editor for Fez, called the Fezzer" (Source)
If you need a simple 2D tile editor, Tiled is a choice that works for me. There are many others available, some tile-based and some not. A couple more examples are Ogmo and Gleed2D. Note that all they do is create data - you still need some code in your game to make sense of the data, which may or may not be already written and available.