We prove that Thompsons group $F$ has a subgroup $H$ such that the conjugacy problem in $H$ is undecidable and the membership problem in $H$ is easily decidable. The subgroup $H$ of $F$ is a closed subgroup of $F$. That is, every function in $F$ which is a piecewise-$H$ function belongs to $H$. Other interesting examples of closed subgroups of $F$ include Jones subgroups $overrightarrow{F}_n$ and Jones $3$-colorable subgroup $mathcal F$. By a recent result of the first author, all maximal subgroups of $F$ of infinite index are closed. In this paper we prove that if $Kleq F$ is finitely generated then the closure of $K$, i.e., the smallest closed subgroup of $F$ which contains $K$, is finitely generated. We also prove that all finitely generated closed subgroups of $F$ are undistorted in $F$. In particular, all finitely generated maximal subgroups of $F$ are undistorted in $F$.
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