The traditional rule is that fewer is used with nouns that can be counted:

fewer people    fewer samples

Less is used with nouns that cannot be counted:

less money    less oxygen

For percentages, use ‘fewer than’ if the thing being measured is a countable noun and ‘less than’ if it is an uncountable noun:

Fewer than 40% of people living in Geelong voted for the change.
Fewer than 80% of the apples are edible.
Less than 5% of the water in the dam was released after the downpour.
Women in the industry earn less than 90% of the wage received by men.