The atoms and molecules that make up your body now, will later make up the bodies of insects, bacteria, fungi, plants, animals and trees.
In buddhist terms your body is made of the five elements (earth, water, fire, air and space).
The existence of atoms and molecules is implicit in the teaching of five elements.
Your body consists of the five elements and it dissolves back into those same elements.
This process takes place every day, not just after death. You lose matter form your body back to the elements in the form of your sweat, your outgoing breath, urine, excrement, saliva, snot, earwax, hair, nails, dandruff, etc...
The formation and dissolution of the body is a traditional object of contemplation. It is mentioned for example in the Satipatthana sutta.
Formation and disintegration of the body is described with great detail in modern science. This knowledge is very useful for a buddhist meditator.
Entomological decomposition of the carcass: http://www.en.wikipedia.org/wiki/Forensic_entomological_decomposition
The buddhist scholar Vasubandhu attacks the atomic theory of Kashmir Vaibhashikas in his writings, and he quotes the Kashmir Vaibhashikas: " We do not say that atoms do not have parts, but we say that atoms nevertheless exist." This is illogical and incoherent for Vasunbandhu, it needs no further comment from him. But acidentally it is the view of modern science about atoms!
In buddhist meditation you think that none of the atoms or elements of your body are You, because you will lose them back to the world around you, and other beings will be made from those very same atoms and elements.