First off, it depends on the type of macro algae. There are some kinds that aren't very palatable to fish or inverts, and others that will drive them nuts.
Second, when you say "going into the main tank" do you mean that it went sexual, released spores, and it's now popping up all over the place? Because if that happens, you'll never get it 100% gone. Best you can hope for is managing it, or replacing the rock and sand. But if it's just that some pieces got sucked into the tank and took root, you can probably remove them by hand.
Someone stop me! Please! But... not just yet...
55 Gal Tropical FW
55 Gal Mixed Reef