Is wood matter?
the short answer... everything is made of matter. in the long run, yes, wood is made of matter
petrified wood is wood that has had all the bacteria killed out of it by mud, sand, volcanic ash or other matter. The matter then turns the wood into stone. Later the stone turns into probably quarts or opal. Usally because its fossilized it keeps its same pattern and the quarts can turn it into different colors.
No, mass is an innate property of matter, and matter can not be destroyed in a chemical reaction. Although after the fire the remains (ashes) weigh less than the original wood, the fire has also produced CO2, Carbon (soot/smoke) and H2O as gases and this is where the mass that was once part of the wood has gone.
Both wood and cotton are composed of plant matter. They are made of plant fibres, organic matter, however you prefer to express it. During processing, say for building, or making clothing, other matter will be added to them, so if you want to look past their botanical origins you'll need to start with the end product.