Windows command language does not have popup windows with buttons but you can use a batch/Visual Basic Script hybrid to do this.
@echo off
echo wscript.quit MsgBox ("Continue?", 4, "Please choose") > yesno.vbs
wscript //nologo yesno.vbs
set value=%errorlevel%
del yesno.vbs
if "%value%"=="6" echo You clicked yes
if "%value%"=="7" echo You clicked no