Scales and modes are difficult to master because there are so many ways to view them.

When I first started, the only mode (a scale relative to a key) I knew was Aeolian because I really only listened to Metallica and that was all I needed. But then I discovered Steve Vai and his extenise use of the lydian and mixolydian modes. I found that each mode has a unique sound.

Anyway, the first thing to do is know that scale backwards and forwards, inside and out. This way you don't have to think about what note comes next. You have to really know its signature sound and get into it. Practice it in all sorts of fingerings and positions. Become one with it. Then when you incorporate it into your music, think about the little tricks and nuances you want to use to bring out the feeling you are trying to create.

This might sound a little preachy, but it works. If you want to avoid making it sound like finger exercises, focus on the chord tones of the progression and use the other notes as passing tones. Don't just go up and down the scale. Think of different ways to get your destination, like big interval leaps (string skipping) or sequences.

Again, the key to success is practice, practice, practice, and a little imagination.