You'll have to use a NativeWindow for that. More info the API docs: http://livedocs.adobe.com/flex/3/langref/flash/display/NativeWindow.html
import flash.display.NativeWindowInitOptions;
import flash.display.NativeWindowSystemChrome;
import flash.display.NativeWindowType;
import flash.display.NativeWindow;
import flash.display.StageAlign;
import flash.display.StageScaleMode;
import flash.geom.Rectangle;
var windowOptions:NativeWindowInitOptions = new NativeWindowInitOptions();
windowOptions.systemChrome = NativeWindowSystemChrome.STANDARD;
windowOptions.type = NativeWindowType.NORMAL;
var newWindow:NativeWindow = new NativeWindow(windowOptions);
newWindow.stage.scaleMode = StageScaleMode.NO_SCALE;
newWindow.stage.align = StageAlign.TOP_LEFT;
newWindow.bounds = new Rectangle(100, 100, 800, 800);
newWindow.activate();