Hi there.

I need some help. I know a handful of scales all over the fretboard in several positions. I find this really helpful when transcribing songs, to understand what is going on.

I have memorized the scales and I play through all of them in every position every day. In addition to that, I use them when i learn songs by ear (which i do every day too).
My problem is that I can't use them while improvising. The problem is not that i don't know which scale to use, because I use what sounds good to me. The problem is that it takes me too long to find the scale on the fretboard (because i have to play through the scale ones to be able to see where the notes are on the fretboard) My goal is to internalize the scales to the point where i automatically can go to these scales when i am to improvise over several chords.

Do any of you know any visualization or memorizing exercise that makes me able to do this? Simply going through all the scales every day has helped me a little bit, but not to the point i want to be.

The way i have learnt these scales is to learn where the root note of the scales are in each position.

Thank you in advance.
Sorry if these are obvious questions mate but it's really unclear where you are with your music theory knowledge.

1. Do you know the major scale?
2. Do you know the minor scale?
3. Do you know the notes on the fretboard?
4. If I had a progression that went A D A E, what scale/s would I use?
5. If I had a progression that went E Am C, what scale/s would I use?
And no, Guitar Hero will not help. Even on expert. Really.
It's not enough to simply learn scales - learn solos using the actual scales so you can get some musical context on how to use them in application. You need to learn some musical phrases along with generic scale knowledge in order to improvise well. The key to soloing well is to understand how to play over a given chord progression - you'll get there a lot faster if you work on learning some examples by great players.

Also, practice improvising entire solos in one small position only - until you really understand it. Then move on to another. Don't hop all over the fretboard until you have mastered each small cluster.
Check out a book called Fretboard Logic SE. Best $20 I've ever spent. I recommend Googling this book, and reading some reviews. You should be able to apply what you already know and work your way through this book pretty quickly and easily. It's actually 2 books in 1.
Sounds like it's time to learn a little theory. And chords.

Start with the basics of Key signature and harmonizing the major scale. Harmonizing the scales you know will be great practice for learning/finding chords all over the fretboard. Take the same approach to those chords as you have with scales.

Further, make sure you learn all 12 major scales, and start "linking" the positions together so you can play them non-stop from the bottom of the fretboard to the top.

Those two things should keep you busy for at least a month.
I think it's telling that you used the word "visualizing" when it comes to scales on the fretboard. Because, of course, music isn't something that we see.

This is, of course, how people learn. But to me, I think that a lot of your problems will be solved if you focus not on visualizing the scales, but on hearing them.

Develop your ear, and you'll probably find that your fingers just go where you want them to go, without you having to think about seeing the scale.