Second seed Nadal, who last played the Basel event in 2004 and returned with a 0-2 record to the St Jakobshalle, needed just 56 minutes to beat the French qualifier.
The Spaniard took full advantage of 11 double-faults off the Herbert serve in what was a frustrating afternoon for the 120th-ranked challenger.
Nadal next plays either 17-year-old Croatian Borna Coric or Andrey Golubev of Kazakhstan. Coric, tipped for a bright future, upset Latvian sixth seed Ernests Gulbis 7-6 (7/2) 6-3 while Golubev advanced over Russian Teimuraz Gabashvili 6-3 6-3.
Federer stands an impressive 51-9 at Basel, where he has figured in the last eight finals. The Swiss is working on a potential blockbuster finish to the 2014 season, with a Davis Cup final, the chance of taking the number one ranking from Novak Djokovic and three more big events to play -- in his hometown, in Paris next week and the eight-man World Tour Finals in London next month.
The nine-time French Open champion looked healthy and fit despite taking antibiotics for two weeks since appendix trouble struck him in China. The 28-year-old will need to have surgery, with doctors unsure of how many more weeks he can go on avoiding the operation.
Belgian seventh seed David Goffin joined Nadal in the last eight as he beat Croatian Ivan Dodig 7-6 (7/0), 6-4.