Make sure your primary boot device in BIOS is Windows Boot Manager while the next suggestion may sound silly but do you have the bootable USB installer plugged into your USB port? If so then you may want to remove it as it sounds you're booting into Advanced Startup Repair mode.
Since when has the issue been with your system? If you can boot into your OS without much trouble you may want to look into performing a
system restore prior to when the issue cropped up. Likewise you can try with a
repair install. Reason for these suggestions is because you can get into Startup Options following
one these methods, i.e manually getting into it thus indicating a possible corruption in your OS installation on your Surface Pro 3.