I've had the same problem... It's complicated cause every time I would say she's beautiful and pretty she'd deny it. Sadly she died but God knows that girl had something special... She just didn't know it yet... R.I.P. Holly... Lost but not forgotten.
She just needs to lean that she is unique. Not everyone can look like the Victoria's Secret models or something but every single person has at least one part on them that is outstanding. Does she have perfect eyebrows? Or gorgeous colored eyes? Maybe her hair is never frizzy? Find that one thing you like the best about her and just tell her randomly 'omg your hair looks perfect today, what did you do to it?' Or something like that. Hopefully she will build confidence over time.
Insecurity is something that takes a person awhile to get past. If you and others tell her how pretty she is often enough, eventually it might build her up until she can see it for herself. Just be persistent.