Fungal infections are very typical in appearance and lead to particular symptoms. So, most of the time, your doctor is able to diagnose you with a fungal infection, based on his/her clinical experience.
In-depth investigation of your disease will be carried out when other - more dangerous - infections have to be excluded or when the clinical aspect of the infection is not that typical.
In the case of a vaginal infection, where infection with Chlamydia has to be ruled out, some mucus will be removed from the vagina and sent to a laboratory for further investigation. Or, in the case of skin and nail infections where the appearance is insignificant, some material will be scratched off the infected area and examined thoroughly under a microscope or through laboratory cultivation.