From Thomas Jefferson Encyclopedia
At the United States Patent Office, paper copies of patent documents are stored in special drawers called "shoes." According to some, the term "shoes" arose from Thomas Jefferson's practice of storing early patent documents in his shoe boxes. This story is probably false.
Henry Remsen, Jr. wrote a memorandum in early 1792, most likely for the benefit of his successor as chief clerk, in which he said the following about patent documents:
Petitions for patents are to be endorsed according to the present mode, the day of their receipt, and noted in the minute book, in which petitions are filed together in the desk up stairs in one of the pigeon holes. In the said desk are filed in another pigeon hole, the petitions decided on; and also the drafts of patents issued, which drafts the law for promoting useful arts directs to be recorded. Some of the specifications are in said desk, and others in the closet.
Monticello research historians have never found any evidence that Jefferson even had shoe boxes. He always ordered his shoes directly from shoemakers, and would have either picked them up or had someone else pick them up; it is unlikely there was a box involved.
Finally, Kenneth W. Dobyns, in The Patent Office Pony: A History of the Early Patent Office, has the following to say about this story:
Printing patents had an interesting and lasting effect on the furniture which was required by the Patent Office. Before patent drawings were printed, examiners, while searching patents, had to look at the original drawings in the draftsman's office in large portfolio cases, such as those shown in the illustration from 1869 on page 173. There were 777 folio cases of original drawings which were safely removed from the draftsman's office in the fire of 1877. But when the drawings, and especially the entire patents, were printed, they were available for search in the examiners' rooms and soon in the new public search room. The necessary new filing system was provided by the shoe cases still in use in today's Patent and Trademark Office. The origin of the term shoe is lost, although every patent examiner knows where his shoes are. Some have attributed the term to Thomas Jefferson, suggesting that he stored his patents in shoe boxes. But we know that the drawings kept in the Patent Office in the preprinting days were of varying sizes and were kept in portfolios from the earliest days. Shoes, as we know them, could only have arisen after all patents were available in small, uniform sizes and could be kept in small, uniform boxes. A complete inventory of the moveable property in the Patent Office was made in 1870, [footnote 1] including numerous portfolio cases, portfolio racks, portfolio drawers, and cases for models, 22,000 volumes of books and 300 spittoons, but no shoes. Augustus Burgdorf, livery stable operator, undertaker and cabinet-maker of Washington, sold portfolios and cases to the Patent Office in 1878. [footnote 2] The first known mention of shoes was on March 28, 1879, when he sold shoe drawers to the Patent Office for $115. [footnote 3] What were called shoe drawers would now be called shoes. Among the many possible origins of the term is that preferred by your guide. Perhaps file cabinets suitable for holding bundles of patents while allowing easy access to search through them were already available before they were needed. Perhaps shoe shops of the day kept their supply of ready-made shoes in wood cabinets containing numerous drawers of just the right size to hold patents, and when the Patent Office wanted to order its first drawers, it ordered shoe drawers from Augustus Burgdorf. Or maybe not." 
- ↑ PTJ 17:385-386.
- ↑ For particulars on Jefferson's shoe purchases, see MB.
- ↑ Kenneth W. Dobyns, The Patent Office Pony: A History of the Early Patent Office (Fredericksburg, Va.: Sargeant Kirkland's Museum and Historical Society, 1994), 193. Text available online at http://www.myoutbox.net/popstart.htm.