$解:(1)∵四边形ABCD是正方形,FD⊥DE$
$∴ AD=CD,∠A=∠DCB=∠ADC= 90°,∠EDF=90°$
$∴∠ADE =90°-∠EDC=∠CDF,∠A=∠DCF=90°$
$在△DAE和△DCF中$
$\begin{cases}∠ADE=∠CDF\\AD=CD\\∠A=∠DCF\end{cases}$
$∴△DAE≌△DCF$
$∴ AE=CF$
$∵四边形ABCD是正方形,AB=6$
$∴易得BD=6\sqrt{2}$
$∵ BD=BF$
$∴CF= BF- BC=BD- BC=6\sqrt{2}-6$
$∴ AE=6\sqrt{2}-6$
$∴ BE=AB-AE=6-(6\sqrt{2}-6)$
$=12-6\sqrt{2}$