Usually if left, the acidic nature of bird poo will etch into the clear coat or surface of the paint. Therefore it is best to remove the marks via machine polishing. This may require some wet sanding of the clear coat too. If severe etching has occurred then the marks will not come out, if you cannot live with it then you may have to consider re-painting the panel!
I think it depends how far they've eaten in to the clear coat. Had a massive seagull splat which only sat on a waxed car for a few hours last summer and I was left with some etching. Fortunately managed to get it out with Meguiars Ultimate Compound by hand