You don't need to clear out any space for the red/yelow lines. As long as your markers are correctly aligned, it will work. (If you watched Etho's videos, he was wrong about this.)
You can also try the flatification pattern (I think that's what it's called): three glass in a row, three bricks in a row underneath them. Mark a horizontally aligned rectangle with three markers and use the filler. It will fill everything below the rectangle, and clear everything above it.
Make sure you do everything in proper order: place markers, right-click a marker, place filler, set pattern, provide power. If you do any steps out of order, the filter tends to get stuck and you need to start over.