解:$(1)$根据题意,得$A'E=AE=3,$$D'F=DF。$
$ $在矩形$ABCD$中,$AB=CD=6,$$AD=BC=4,$$∠ B=90°。$
∵$AE=3,$
∴$BE=AB-AE=3,$
∴$CE=\sqrt {BC^2+BE^2}=\sqrt {4^2+3^2}=5。$
∵四边形$ABCD$是矩形,
∴$AB// CD,$
∴$∠ AEF=∠ CFE,$由折叠可知,$∠ AEF=∠ CEF,$
∴$∠ CFE=∠ CEF,$
∴$CF=CE=5,$
∴$DF=CD-CF=6-5=1。$
由折叠可知,$D'F=DF=1,$即$D'F $的长为$1。$
$ (2)$当$AE=\frac {13}{3}$时,四边形$AEA'F $为菱形。理由如下:
根据题意,得$A'E=AE,$$A'F=AF。$
∵四边形$AEA'F $为菱形,
∴$AE=AF=A'F=A'E。$
$ $设$AE=x,$则$A'E=AE=AF=x,$$BE=AB-AE=6-x,$
∴$CF=CE=\sqrt {BC^2+BE^2}=\sqrt {16+(6-x)^2},$
$DF=\sqrt {AF^2-AD^2}=\sqrt {x^2-16},$
∵$DF+CF=CD,$
∴$\sqrt {x^2-16}+\sqrt {16+(6-x)^2}=6,$
$ $解得$x=\frac {13}{3},$即$AE=\frac {13}{3},$
∴当$AE=\frac {13}{3}$时,四边形$AEA'F $为菱形。