Fibre Optic transmission uses a coding technique of one sort or another for communication. Lasers are not amplitude modulated, rather, they are switched on and off at very high data rates to represent bit patterns.
The receiver uses a device, commonly a photodiode, to receive the beam. Both ends of the fibre must be cut, polished and precisely matched to the interface and connector type, otherwise your optical link-loss will be huge and will most likely fail over anything but the shortest of links.
Terminating fibre is a tricky prospect without the right tooling and experience. The type of fibre whether multi-mode or single-mode must match the laser/ receiver pair exactly, any misalignment means severe signal loss. The wavelength of the laser will also play a part depending on several factors.
Remember that unless you are planning on using smoke signals, communication is a two way thing, to that end, you actually require two lasers, two receivers and two fibre links, one set for each direction.
If your link distance is reasonable, say less than 100M, you would be better to buy a couple of cheap FDDI transceviers and modify those to suit your application. Cheap multi-mode fibre can then be used between them. You can either buy a small termination starter type kit and do it yourself, or better still, buy your fibre from a half decent networking company, and get them to terminate your fibre for you.
Cheap in this context is a relative concept. Fibre-optic communication is expensive.
I don't want to pour cold water on your enthusiasm, but rolling your own transceivers capable of anything near 3Mbps is a non starter. Put your time and energy into your project in a sensible way, and use purpose built and tested transceivers.
rgds
I forgot to mention that as you have gotten as far as the optical link in your project, I am assuming that you have already taken care of the protocol translation, but if you haven't, then you will also have to take this into account in your design as well.
HD3B uses clock recovery for example, so you would need to take account of that etc etc.