There isn't a magic way to make the windows command prompt suddenly use / instead of \, it's a hardcoded thing that's been that way for 20 years. Windows understands both \ and /, but since / usually means commandline options, most windows commandline programs will refuse to accept a path that uses /'s.
If there are too many scripts to change by hand, you may wish to use automated tools like sed to convert / to \. Be careful to only convert the relevant forward-slashes.
ls \temp or ls temp specify a relative path, ie search in the current directory for temp and list the items
ls /temp specifies an absolute path from the root! ie / so you are asking him a completely different thing. If you want the temp on your c drive, you need to specify /cygdrive/c/temp !!
Or, just do as Corona688 says, and push 'man sed' or man tr