If you want to create sub-folder in SD Card of Android Emulator, Android Debug Bridge(adb) can be used. Android Debug Bridge(adb) is a versatile tool lets you manage the state of an emulator instance or Android-powered device.
With Android Emulator running, start a Terminal (in Linux), switch to the <android sdk>/tools folder. type the command:
$./adb shell "mkdir /sdcard/myFolder"
<android sdk> is the location of your installed android sdk.
myFolder is the folder you want to create.
Related article: Create SD Card in Android Emulator and copy files into, in Eclipse, Emulator and DDMS.