The noun (Substantiv/Nomen) Flecken is feminine in German. Therefore, the correct definite article in the nominative singular is die. So, you say: die Flecken.
(stains)
Mehrere kleine, meist unsaubere Stellen auf einer Oberfläche.
Several small, usually dirty spots on a surface.
Das Kleid hat viele Flecken.
The dress has many stains.