Ventilation is the key here. on bright winter/spring days open the doors/vents to get a through breeze.
remove and bin[not compost bin though] any fallen leaves that might be harbouring fungal spores.

hope this helps.

A rather quicker way is also rather more dangerous. Jeyes fluid in a weak solution can be used to wash out the greenhouse but not if there are plants that cannot be moved out. Jeyes is a herbivore and an insecticide. Not at all a green way of doing it. It kills benificient as well as nasty insects and after treatment the green house has to be thoroughly washed out of all traces. Not really recommended for serious gardeners except in extreme circumstances. If you should decide that drastic measures are needed, when you have used, and got rid of, the Jeyes you should follow SBgirl's advice to prevent it springing up again.

Only did the Jeyes method once and either I have very sensitive skin or it is nasty stuff but I had sores from the splashes that took an age to heal. But I could breathe really freely :o)