I had the same problem and heard that Blonde Naso tangs eat it so I gave one a shot. Yup. He mowed them down in no time. Pretty much the only fish that ever touched it (in my experience anyway).
edit: Scratch that ! Sorry, I got Halimeda confused with another macro algae that Blonde Naso Tangs eat. I in fact do not know what eats Halimeda. I do have it in my tank and no one eats it
Pretty much just manually prune but thankfully they are easy to prune.