The deal with a bike is there is no hard and fast written rule on how a bike depreciates.
So fair market value is what a regular joe would be willing to pay for the bike in its current state. (ebay is a good guide for this).
A company can not agree the final fair market price before the bike reaches the end of it's lease period.... otherwise the bike 'deal' would be seen as a benefit-in-kind and as such the 'tax man' would require the saving to be repaid.
You do need to make a payment to your company to make the bike yours... this is the only way to transfer ownership of the bike. Theoretically this figure could be as low as a penny.
Assuming your company has run their cycle2work scheme with CycleScheme (the largest provider of C2W) then it is likely that the fair-market value will be payable direcly to CycleScheme and not your employer, unless your employer has changed the standard cyclescheme hire agreement (many employers do).
Assuming you do need to pay your fair market value to cyclescheme.. then they will ask you to go back to your LBS with your bike to get it valued using cyclescheme's sliding scale.
good condition bikes are worth more than shagged ones.
I would suggest you cover your bike in insulation tape... get it muddy and pop on some worn out tyres and hey presto a low fair market value awaits you (PS shop staff at your LBS do like biscuits)
;]