Sometimes an invention employs a proprietary branded product and the only way to describe and claim it is to refer to it by the trademark.  This presents unique problems for the patent prosecutor because a branded product is usually not in the control of the patent applicant, and thus can change after the application is drafted and filed.  This is a particular problem in the claims, where the changing scope could invalidate the claim or make the claim impossible to infringe.  The MPEP addresses the use of trademarks in a patent application:

VELCRO appears the claims of 2077 patents, TEFLON appears om the claims of 3585 patents, ETHERNET appears in the claims of 7425 patents, and JAVA appears in 3690 patents.  For examples, see U.S. Patent No. 6,959,462, Claim 2 (VELCRO); U.S. Patent No. 8,485,489, Claim 12, and 8,062,571, claim 4 (TEFLON); U.S. Patent No. 8,457,003, Claims 2, 3, U.S. Patent No. 8,422,359, claim 10, and U.S. Patent No. 8,363,655, claim 5 (ETHERNET); and U.S. Patent No. 8,330,862, Claim 4, and U.S. Patent No. 8,254,757 (JAVA).