Can I recover my system by reinstalling Mountain Lion from boot USB on my failed Mavericks OS?

I have an iMac 8.1 with SSD and Mavericks installed.
Upon startup I get the flashing folder with questions mark, that tells me that it cannot boot.
I have a Mountain Lion boot USB, and with that I checked with Disk Utility if my disk can be repaired.
After verifying the disk, it tells me everything is fine with the disk.
So I guess the OS on the disk is damaged.
Can I use the Mountain Lion boot USB and reinstall OS X, and thereby preserve my files (settings are not most important).
I do have most of my data on an external HDD, but would have some valuable files the SSD (photos, documents and bookmarks).

Have you tried  booting while holding down the Option key?
Startup Manager: How to select a startup volume

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