Biofuels are derived from living matter and the waste it produces. Fossil fuels come from matter that was deposited millions of years ago in the earth (land or sea bed). The crops developed for biofuels absorb carbon as they grow which offsets the CO2 emitted into the atmosphere when the plant matter is burned. On the other hand the matter used for fossil fuels harbors carbon that has been stored for millennia which is released as CO2 when burned.
There are two ways plant energy (captured by the process of photosynthesis) can be converted into biofuels. The first is by fermenting plants such as corn, sugar and wheat to produce an alcohol called bio-ethanol. The fermenting process is similar to that used to make wine. This is then usually mixed with petrol before use.
The second way is to use vegetable oils, from say soyabean or palm plants, by heating and reducing the oil's thickness. This can then be used as engine fuel. These vegetable oils can also be put through a chemical process called transertification to produce biodiesel.
On the peripherary the biofuel approach appears to be carbon neutral and clean. Though it is a better alternative to fossil fuel, unfortunately the energy return on energy invested is very low and the carbon footprint very high compared to alternative energy derivatives such as solar or wind power.