There are two parts to this question or issue, one is about meditation the other is about chakra's, ie what really are they.
Most people have heard the term or word meditation, but may not have a clear idea of what it means.
It has always had a slightly mysterious aura bout it, probably because it is seen as an Eastern prayer technique, something the west is just beginning to understand.
That really isn't true, but so long as the perception is there, that will persist.
The word chakra is probably not as well known, but people have often seen what is commonly depicted as a symbol of chakras, a sort of really nice flower symbol or emblem.
To explain a chakra meditation, it is necessary first to understand what a chakra is.
It is more easily explained by thinking of it in terms of the body's energy systems.
Many philosophies of the way the human body and mind are related explain them in terms of energy.
Acupuncture, Tai- chi and Chi Kung are some of the best known ones, but Chakra's are also widely used as an explanation.
People think of the body as having a number of energy centers through out the body, ranging from the top of the head to the feet, each of these energy centers has its own name, and its own energy source, and in some traditions, its own color as well.
Each chakra is independent of the others, but they all function together to stabilize and boost your bodies energy levels, and in turn your own health and well being.
A chakra meditation in effect spend s a bit of time focusing on each chakra of the body in turn, and uses the power of your imagination to boost its energy levels.
It will also focus on the line of the body that the chakra's run through, in order to boost their maximum effectiveness