Usually when a person refers to a "three-dimensional pentagon," he is referring to a regular dodecahedron. A dodecahedron is a solid made of 12 flat faces, and a regular dodecahedron is made of 12 regular pentagons.
A three-dimensional pentagon could also be referred to as a pentagonal prism. A pentagonal prism is made by a pentagon being extruded so that it forms a five-sided elongation capped with two regular pentagons. (A regular polygon is one with sides of equal length and equal angles in between them.) This is similar to the way a rectangular prism or a cylinder is formed.