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I assume that modal is a child component.

You need to send component event from child to parent and in parent event handler close the modal.

In Parent

<aura:handler name="myComponentEvent" event="c:componentEvent" action="{!c.handleMyComponentEvent}"/>

Parent controller

({
    handleMyComponentEvent : function(component, event, helper) {
        component.find("overlayLib").notifyClose();
    }
})

You can optionally stop propagation of the event here using

event.stopPropagation();

if you do not want your event to propagate further

In child

<aura:registerEvent name="myComponentEvent" type="c:componentEvent"/>


handleUploadFinished: function (component, event) {
    var uploadedFiles = event.getParam("files");
    console.log(uploadedFiles[0].documentId); // See? it works.
    var myEvent = component.getEvent("myComponentEvent");
    myEvent.fire();
}

And event itself

<aura:event type="COMPONENT">

</aura:event>

Obviously with desired event name, in example

componentEvent