Method including positioning a source die or a destination site to compensate for overlay error

A method, comprising:

• bonding a first source die to a first destination site of a destination substrate, wherein:
• the first source die includes a first source active region and a first source boundary region, wherein the first source active region includes a first source active contact pad, and the first source boundary region includes a first source metrology pattern including a first source alignment mark, and
• the first destination site includes a first destination active region and a first destination boundary region, wherein the first destination active region includes a first destination active contact pad, and the first destination boundary region includes a first destination metrology pattern including a first destination alignment mark, and
• after bonding, the first source active contact pad contacts the first destination active contact pad;
• collecting first radiation data regarding at least portions of the first source metrology pattern and the first destination metrology pattern within a first radiation area, wherein collecting the first radiation data is performed after bonding the first source die to the first destination site, and within the first radiation area, the first source alignment mark does not directly overlie or directly underlie any alignment mark of the first destination metrology pattern;
• analyzing the first radiation data to determine a first overlay error between the first source die and the first destination site;
• and
• adjusting a position of a second source die or a second destination site of the destination substrate to compensate for the first overlay error between the first source die and the first destination site.