Blind bake pie crust by recipe directions and set aside.
Clean beets thoroughly and remove tops and roots.
Wrap each beet individually in foil.
Roast in 275 degree oven for 4 hours or until tender.
Remove skin by hand while warm.
Cut beets into cubes, reserving as much juice as possible and set aside.
Melt 2 tbsp butter in nonstick skillet.
Saute onions and fennel with thyme until onions are translucent and set aside.
Melt remaining butter in skillet.
Add flour, stirring with wood spoon until smooth.
Add milk slowly, stirring until each addition is combined and smooth.
Add chevre, stirring until fully melted and incorporated.
Return onions, fennel and beets to skillet with cream sauce.
Smooth filling into crust.
Bake in 375 degree oven for 15 minutes or until filling is hot throughout.