You may try using glScissor
like this:
glEnable(GL_SCISSOR_TEST);
glScissor(windowPosition.x, windowPosition.y, windowWidth, windowHeight);
// here put your draw method of your window and objects inside it
glDisable(GL_SCISSOR_TEST);
More info : http://www.opengl.org/sdk/docs/man/xhtml/glScissor.xml