<p>I would like to make custom insoles for my wife.</p>

<p>This company makes a flexible filament that will be soft to stand on:
<a href="http://recreus.com/en/" rel="noreferrer">http://recreus.com/en/</a></p>

<p>I do not currently own a printer.</p>

<p>How can I measure her feet and transfer the measurements to the printer?
(one of these comes to mind: <a href="http://www.eggheadtoys.com/pin-art/" rel="noreferrer">http://www.eggheadtoys.com/pin-art/</a>)</p>

<p>How can I measure the inside of the shoe?</p>

<p>What kind of printer can print with the flexible filament?</p>

Many questions in one post, but I'll address only the first. Consider to use a shoe with a flat insole, perhaps even what is commonly called a flip-flop. If your objective is to perfectly match the curve of her foot bottom, this should work. Apply a layer of polymer modeling clay, plasticine or similar material. It should be warm enough to permit her foot/feet to settle in and push enough material away to remove any voids. If voids appear, one could then add a few blobs and repeat the pressure.
Obviously some will ooze from the sides, which will have to be trimmed away. Trim a sufficient amount to fit her regular shoes and you'll have a reasonable match of the necessary fit.
The resulting shape can then be scanned with a 3d scanner and converted to a 3d model. Even if the clay is excessively thick, the typical 3d model editor can slice away the excess, although one would have to make an almost arbitrary judgement for the location of the slicing plane.
Another option comes to mind. There are various silicone molding products. I've used one from makeyourownmolds.com that is of a consistency of frosting. When mixed together and applied, it makes a perfect duplicate of the item, in reverse. Another product sold at the local HobbyLobby is a similar molding compound that is more akin to the modeling clay.
Both compounds will release easily from skin, are non-toxic and would provide a more durable model from which to scan.
I think one difficulty you may have is how to determine the correct foot pressure and posture to achieve the desired results. The modeling clay would give you more support and probably be more accurate. If your objective is to provide the same support as a bare foot, the silicone molding method would be more accurate.
If you stretch the concept even further, once you have the silicone or clay mold, you would be able to use the pin-art concept. The idea of measuring each tiny pin is mind-boggling, though.