One way of achieving this is by composing your desired 'cookie' with SKSpriteNodes, then creating a texture to render it 'as is' to a new SpriteNode, which will then blend as a whole with the scene.
In this simple example I've used a rectangle to highlight, but you could make that node any node type or image, and adjust the alpha value accordingly.
Draw your scene as normal, then add this code:
// dim the entire background of the scene to 70% darker
SKSpriteNode* background = [SKSpriteNode spriteNodeWithColor:[UIColor colorWithRed:0
green:0
blue:0
alpha:0.7]
size:self.frame.size];
// make a square of 100,100. This could be an image or shapenode rendered to a spritenode
// make the cut out only dim 20% - this is because no dim will look very harsh
SKSpriteNode* cutOut = [SKSpriteNode spriteNodeWithColor:[UIColor colorWithRed:0
green:0
blue:0
alpha:0.2]
size:CGSizeMake(100,100)];
// add the cut out to the background and make the blend mode replace the colors
cutOut.blendMode = SKBlendModeReplace;
[background addChild:cutOut];
// we now need to make a texture from this node, otherwise the cutout will replace the underlying
// background completely
SKTexture* newTexture = [self.view textureFromNode:background];
SKSpriteNode* newBackground = [SKSpriteNode spriteNodeWithTexture:newTexture];
// position our background over the entire scene by adjusting the anchor point (or position)
newBackground.anchorPoint = CGPointMake(0,0);
[self addChild:newBackground];
// if you have other items in the scene, you'll want to increaes the Z position to make it go ontop.
newBackground.zPosition = 5;