This lesson will help you in your quest in breaking out of those standard "Box" shapes and be able to use your entire fretboard. One way is to use what are called "Linear Scales" which are using scales on one string up and down the neck in a "Linear" fashion.
This first 2 examples are written out in a triplet pattern. Make sure that you are using strict alternate picking and you are accenting the first beat of each triplet group.
The second examples are a variation on the first ones and makes you see a scale as a straight line.
Once you have memorized these scales, apply this concept to all the major scale modes as well as any other scales you use most often. Use different rhythm groups and picking techniques for variations. Your ultimate goal is to memorize all scales in all keys.