Right click on your MovieClip item in the library. Select the "Export for ActionScript". This will then fill in the class field. Selected Ok twice. Lets say your class was called 'mcSquare'
var mySquare:mcSquare = new mcSquare();
addChild(mySquare);
To then fade them in simply set the alpha of the mySquare to 0 (directly before or after addChild) and then tween the alpha of the clip to 1.
EDIT:
Label the movieclips in your library mc0, mc1 and so on. In this example up to mc6.
const MAX_ITEMS:uint = 7; //if you have seven movielips
var container:Array = new Array();
for (var i:int = 0;i < MAX_ITEMS;i++)
{
var className:Class = getDefinitionByName("mc"+i) as Class;
var newMovieClip:MovieClip= new className();
container.push(newMovieClip)
}
for (var k:int = 0; k < MAX_ITEMS;k++)
{
var myClip:MovieClip = container[k] as MovieClip;
myClip.alpha = 0;
stage.addChild(myClip);
//apply tweening to myClip
}