A process for manufacturing a MEMS device includes forming a first structural layer of a first thickness on a substrate. First trenches are formed through the first structural layer, and masking regions separated by first openings are formed on the first structural layer. A second structural layer of a second thickness is formed on the first structural layer in direct contact with the first structural layer at the first openings and forms, together with the first structural layer, thick structural regions having a third thickness equal to the sum of the first and the second thicknesses. A plurality of second trenches are formed through the second structural layer, over the masking regions, and third trenches are formed through the first and the second structural layers by removing selective portions of the thick structural regions.