Yes, there are. The protection of company names falls within the remit of the Federal Commercial Registry Office and general enquiries should be directed to them. Actual applications for registration should be directed to the cantonal or local department of commerce.
Plant varieties and their designations are protected by the Plant Varieties Rights Office within the Federal Office for Agriculture. This office is also responsible for AOCs (appellations of controlled origin) and PGIs (protected geographical indications).
Roundtable on the protection of computer-implemented inventions