To face Isaac (Boss) you need to either kill the boss "It Lives", or enter an angel room after killing Mom's heart. He will appear after beating the Cathedral level.
This boss is actually pretty easy, but it's important to know how Isaac attacks and how to minimize damage taken. There are three phases to his attacks.
Phase 1 - Isaac will fire rapid tears at you. These can easily be avoided if stood in the right place. They will fire in rows with spaces between each row.
Phase 2 - Same as 1, but Isaac spawns minions which fire blood tears in triplets. Also avoid the light beams.
Phase 3 - The boss will now move much faster and begin to teleport. When he does teleport, he will release multiple beams of light covering almost the entire floor. You can avoid this by standing right in a corner.