Your original statement is:
Microwave energy is an efficient heating tool for the materials possessing dielectric molecules such as water.
In discussion you have clarified that water is a dielectric molecule which you mean to show can be a component of other materials.
Given this, I would say your statement is quite correct, but could be considered ambiguous to some audiences. This is because it is not completely clear if water is an example of the dielectric molecules, or an example of the materials. Likely this would be understood perfectly by the scientific community, but not necessarily to a student or a "layman".
Also, because you use the definite article and say "the materials" it infers you are talking about something specific, such as a limited set of materials that you have previously referred to. If you intend to state that microwave energy is efficient for heating any material that contains water molecules then you should omit "the".
Lastly, although I'm perhaps being picky here, I'm not sure if microwave energy should be referred to as a tool? A microwave oven would certainly be a tool.
With these points in mind I would suggest the clearest statement would be:
Using microwave energy is an efficient method for heating materials that possess dielectric molecules such as water.