(1) 证明:过点$D$作$DN\perp AB$于点$N。$因为$DE\perp BC,$$DF\perp AC,$所以$\angle DEC = \angle DFC = 90^{\circ}。$又$\angle C = 90^{\circ},$所以四边形$CFDE$是矩形。因为$AD$平分$\angle BAC,$所以$DF = DN。$因为$BD$平分$\angle ABC,$所以$DE = DN,$所以$DF = DE,$所以四边形$CFDE$是正方形。
(2) 解:因为$\angle C = 90^{\circ},$$AC = 3,$$BC = 4,$所以$AB = \sqrt{AC^{2}+BC^{2}} = 5。$设$\triangle ABC$的内切圆的半径为$r,$则$S_{\triangle ABC}=\frac{1}{2}AC\cdot BC=\frac{1}{2}(AC + BC + AB)\cdot r,$即$\frac{1}{2}\times3\times4=\frac{1}{2}\times(3 + 4 + 5)\times r,$解得$r = 1。$故$\triangle ABC$的内切圆的半径为$1。$