Most of the time when measuring VOCs with GC/MS it is using purge and trap or headspace. This should give a fairly sharp peak for CO2 which could be subtracted from the total. Also most of the time GC/MS is used for targeted analysis where each individual analyte is calibrated from standards, but if you are trying to measure total just by chromatographic peak area with no target analysis then it will not be that accurate because each analyte has a different response factor so that 1000 area counts for Benzene may be equal to 5ng and 1000 area counts for acetone may be equal to 10ng.
What type of VOCs are you wanting to quantify? Do you need to include methane and methanol, or are you interested in the heavier items such as acetone, benzene, chloroform, ect?