You always have to extract mycotoxins from the substrate or material in which the fungus growth before you can (chemically) the determine the amount. So any paper on chemical analysis of mycotoxins, will contain a section on its isolation. Whether that is applicable in your situation, depends on your aim.
Yes you can extract. Please see "A polyphasic study of Aspergillus section Flavi isolated from corn in Guangxi, China- a hot spot of aflatoxin contamination"