<apex:page controller="popup">
    <apex:form >
        <apex:commandButton value="Show Pop up" action="{!showPopup}" rerender="popup"/>
        <apex:pageBlock >
            Lorem ipsum ..... dummy stuff to show the popup is above content
        </apex:pageBlock>
 
        <apex:outputPanel id="popup">
            <apex:outputPanel styleClass="customPopup" layout="block" rendered="{!displayPopUp}">
                Lorem ipsum <br/><br/><br/>
                
<!--                <apex:iframe src="apex/popuptest?param='new'" scrolling="true" id="theIframe"/>-->
                <apex:commandButton value="Hide Pop up" action="{!closePopup}" rerender="popup"/>
            </apex:outputPanel>
        </apex:outputPanel>
 
    </apex:form>
 
    <style type="text/css">
       .customPopup{
            background-color: white;
            border-style: solid;
            border-width: 2px;
            left: 50%;
            padding:10px;
            position: absolute;
            z-index: 9999;
            /* These are the 3 css properties you will need to tweak so the pop 
            up displays in the center of the screen. First set the width. Then set 
            margin-left to negative half of what the width is. You can also add 
            the height property for a fixed size pop up.*/
            width: 500px;
            margin-left: -250px;
            top:100px;
        }
    </style>
</apex:page>

public class popup {
 
    public boolean displayPopup {get; set;}
 
    public void closePopup() {
        displayPopup = false;
    }
 
    public void showPopup() {
        displayPopup = true;
    }
}