using standard microbiology techniques. One example among many would be: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769566/
Once you have isolates on agar plates, it is easy to purify them down to clonality by streaking a diluted spore suspension (or mycelium fragments) on a plate, and pick individual colonies.
Preparation and maintenance of pure culture by spore suspension or mycelium fragments is of prime importance. then you can use mycelium form this culture for DNA extraction.