Having linked together a series of chords, the next step is to pick out individual notes and play them as scales. To play any sort of scale structure, or melody, it is important to develop the ability to play notes evenly, and build up timing control. To play a scale, the left hand must be able to pick out each individual note clearly. To be effective, the right hand must be co-ordinated with the left. These skills are vital in laying the foundations of playing correctly.

Introducing scales
Melody and harmony are based on the organization of individual notes into an ordered succession. This sequence is termed a SCALE. Most scales used in western classical music are made up using seven notes, with fixed intervals within an octave.
Scale positions
The guitar is constructed in such a way that the same notes can be played in different positions in the fingerboard. The same scale can be played by moving along one string or across different strings.
RHYTHM & TIMING
Rhythm and timing is the framework within which the notes are placed to define their character and effect. Up until now, chords and scales have been played as a sequence of movements without any sort of strict time value. However, virtually music is played or written down using an ordered system for the duration and positions of musical sounds. Once the left hand has be come reasonably comfortable when forming E major and A minor chord shapes, the next logical step is to develop smooth and even movement between chords, creating a basic rhythm structure. With practice, co-ordination between the hands will gradually improve, paving the way for playing chords changes in a set period of time.
Tempo & crochet speed
As the beat in music can be vary in speed, the amount of time between each beat changes: this is referred to as the tempo. The crochet is often used as a reference point for tempo. A crochet written down with a number next to it indicates how many are play each minute.
For example, if a crochet is marked as the picture above, the rate of movement in the music is one crochet beat per second.
Metronomes and sound sources
Using a source to provide an even beat can be of great help when trying to acquire basic rhythm co-ordination. The "click" from a metronome, or a regular beat from a drum machine or sequencer can be adjusted to provide a comfortable speed to strike notes and individual notes. This will help to develop the ability to coincide right-hand movement with the beat.
Some exercise for scales

Here's a simple major scale pattern. Use the metronome on the right side of the page and set it to 60 bpm. Play according to the picture across the fingerboard. The red dotes indicate the root of the scale. The root of this scale pattern would be F#.
Playing in time
Play each note on each metronome "click". Then, with the same speed, play 2 notes per "click. And it goes on and on.

This would be minor scale. It depends on where do you start.
Happy practicing!
Information adapted from:
-The Complete Guitarist book by Richard Chapman
-Photos: