Good answers already, but just to add my 2 yen:

1. To withdraw money, the best ATMs are at Japan Post offices. Convenience stores ATMs do not always accept withdrawals, Japan Post ATMs always do, according to my experience. Japan Post offices are open less often, though.
2. Some places take a fee for credit card (see my picture below). It is quite rare though.

Good answers already, but just to add my 2 yen:

1. To withdraw money, the best ATMs are at Japan Post offices. Convenience stores ATMs do not always accept withdrawals, Japan Post ATMs always do, according to my experience. Japan Post offices are open less often, though.
2. Some places take a fee for credit card (see my picture below). It is quite rare though.

Wikivoyage has a list of banks and ATMs showing what cards they accept and how much they charge in fees (yes some are free).