$解:∵ \sqrt{x}+ \sqrt{\frac{1}{x}}=\sqrt{6},$
$∴\ (\sqrt{x}+ \sqrt{\frac{1}{x}})²=6,$
$即x+\frac{1}{x}+2=6,\ $
$∴x+\frac {1}{x}=4,$
$∴ (\sqrt{x}- \sqrt{\frac{1}{x}})²$
$=x+\frac{1}{x}-2$
$=4-2$
$=2,$
$∴ \sqrt{x}-\sqrt{\frac{1}{x}}=±\sqrt{2}$
$∵ x>1,∴x>\frac{1}{x},$
$∴ \sqrt{x}>\sqrt{\frac {1}{x}} ,$
$∴\sqrt{x}-\sqrt{\frac{1}{x}}=\sqrt{2} $