Hi Carlos,
Thanks for the help.
I talked to a support engineer at FTDI and he said the task of writing a driver for the chip was complex and required previous experience of writing USB drivers and extensive USB knowledge, which I don't have.
The Serial to USB converter was inside a machine that was still under warranty so could not be changed.
For people who may be encountering the same problem, I have decided to solve it by using a Raspberry Pi as the bridge between the machine and the microcontroller. FTDI provide a Linux driver for their chip so the driver problem has been avoided.