Fender trim suggestions

[Glockwarrior]

I finally got another T4R yesterday, it's a 99 SR5 4wheel. I have always wanted to take the running boards and trim off my 1st runner and never did.
Tonight I took them off my new one and it looks great but where the fender moulding was it looks alittle rough.
What have you all done to make this right?
Pics would be great too

 

[TheKorstjens]

Buff it out with rubbing compound,polish, clay bar and wax