Your code works for me:
$Version
(* "11.1.0 for Microsoft Windows (64-bit) (March 13, 2017)"*)
f1 = FourierTransform[
Piecewise[{{1, x^2 + y^2 <= 1}, {0, x^2 + y^2 > 1}}], {x, y}, {u,
v}]
(* BesselJ[1,Sqrt[u^2+v^2]]/Sqrt[u^2+v^2]*)
Plot3D[f1, {u, -7, 7}, {v, -7, 7}, PlotRange -> All]