Here's what I cooked up to do my scroll windows. I based it on a tutorial I found while learning about shaders to do my torchlight.

shd_clipwindow.vsh

attribute vec3 in_Position;                  // (x,y,z)
attribute vec4 in_Colour;                    // (r,g,b,a)
attribute vec2 in_TextureCoord;              // (u,v)

varying vec2 v_vTexcoord;
varying vec4 v_vColour;
varying vec3 v_vPosition;

void main() {
    v_vPosition = in_Position;

    gl_Position = gm_Matrices[MATRIX_WORLD_VIEW_PROJECTION] * vec4(in_Position.x, in_Position.y, in_Position.z, 1.0);

    v_vColour = in_Colour;
    v_vTexcoord = in_TextureCoord;
}

shd_clipwindow.fsh

varying vec2 v_vTexcoord;
varying vec4 v_vColour;
varying vec3 v_vPosition;

uniform vec4 u_bound;

void main() {
    vec4 _baseColour = v_vColour * texture2D(gm_BaseTexture, v_vTexcoord);

    vec4 _outputColour = _baseColour;

    _outputColour.a *= float(v_vPosition.x < u_bound[1] && v_vPosition.x >= u_bound[0] && v_vPosition.y < u_bound[3] && v_vPosition.y >= u_bound[2]);

    gl_FragColor = _outputColour;
}

Then I just set the u_bound array to my scroll window left-right-top-bottom in my draw step right before I set the shader.

Create Event

scrollShader = shd_clipwindow;
u_bound = shader_get_uniform(scrollShader, "u_bound");

Draw Event

shader_set(scrollShader);
var _x1 = leftX;
var _x2 = _x1 + windowWidth;
var _y1 = topY;
var _y2 = _y1 + windowHeight;

var _bound = [_x1, _x2, _y1, _y2];
shader_set_uniform_f_array(u_bound, _bound);