Removing Ruined Portals From a World You Already Started

Understand the Limitation First

The mod only affects chunks generated while it is installed. A world you already explored has ruined portals baked into its region files, and the mod will not touch them. If you want them gone, you have to deal with the existing ones yourself.

Manual Removal in Creative or With Commands

Switch to Creative mode or enable cheats, then locate each ruined portal. Break the obsidian and crying obsidian frame, remove the gold block, and clear the lava. The loot chest can be broken or emptied. If you would rather not hunt them down, use the /locate structure command with the ruined portal structure ID to get coordinates, then teleport there and dismantle it. Repeat until the area you care about is clean.

Prevent New Ones Going Forward

Once the mod is installed, any fresh chunks you generate will be free of ruined portals. So the practical workflow is: clean up the region you have already visited, then let the mod handle everything beyond that. If you plan to explore far, do the cleanup only around your base and any builds you care about — the rest of the old terrain is usually not worth the effort.