Yesterday I was taking my boat out of the water and forgot to raise the motor  

It scrapped the lower part pretty good. Can I file it down and be okay? Nothing was cracked.

I hope I learned and never do that again.

And yes I am a newbie and this is only the second time to have my boat in the water.

There is a  part called a scag repair kit. You can find it in bass pro catalog. If its only scratched off a little I would file it down since those repair kits are ugly! As long as its only an inch or so it wont bother your performance.

Don't feel like the Lone Ranger on this one.  I have done it, and I'm sure alot of others have as well.  With a file and a little paint as good as new.  If you happen to bounce your skeg off the ramp like I did, 100 bucks at the dealer, and it's good as new.

Yes I would have to agree, every boat owner has had this happen at one point or another, due to their fault or someone else's.

You can file it and paint it or you could purchase a skeg protector, drill a couple of holes and be done with it....I think they are about 75 bucks...and this will assure no damage to the original skeg will happen again.

Just a short story about something that happened to me one time in a boats first time on the water.  It was my father-in-laws brand new Thunder Jet 19' Sport Jet boat.  We were in the Coquille River in Bandon Oregon and I went out with him to kind of watch over him and make sure things went smoothly his first time out.  It was him, me and his older brother of about 60.  We were done hanging up and losing trolling gear for the day so we took it in to the dock and told his brother to go back the trailer into the water.  I stayed on the boat with the father-in-law to help him get it lined up and on the trailer...it took forever and he finally got it up on the trailer all the way.  I told him to go up and secure the winch hook to the boat and give it a couple of cranks to make sure we were up in the trailer snug.  When he got up he did something with his hands that indicated to his brother to pull out, and he did-before the boat was hooked up...I was in shock and afraid to yell at him to stop because I was afraid it would make the aluminum boat slide right off the UHMW plastic covered bunks and slide off the trailer on the boat ramp.  We would have likely made it out OK...I have seen it done before as long as the driver is smooth pulling out.  My father-in-law on the other hand yelled STOP...and the boat slid right off the trailer and onto the boat ramp.  It totally destroyed the trim plate and the transducers for all the electronics, not to mention scratched up the bottom pretty good.  We had a hell of a time getting it trailered again.  My father-in-law was pi$$ed.  I was too.  His poor brother to a butt chewing for the entire hour ride home.  It was a lesson learned and needless to say my father-in-law got pretty good at trailering a boat by himself after that...unless I was with him.  He doesn't trust anyone now except me to help him.  It was embarrassing as hell.  

I'm not sure how others do it but when i'm loading my boat, i like to use the outboard to get it up on the trailer as far as possible so i don't have to crank the winch as much.  When i do this, i always trim the motor up to where the de-aeration plate (?) is just below the surface.  This also assures me the motor is up enough before we pull it out.