A request XML packet that deletes certificate should include the remove operation node:
<packet version="1.4.2.0">
<certificate>
<remove>
...
</remove>
</certificate>
</packet>
The remove node does not have a separate type, it is nested within type CertificateActionRequest (certificate_input.xsd). The remove node has the following graphical representation:

Remarks
1. The filter node allows specifying multiple certificate names, which gives you opportunity to delete several certificates within one remove operation.
<packet version="1.4.2.0">
<certificate>
<remove>
<filter>
<name>cert_1</name>
<name>cert_2</name>
<name>cert_3</name>
<name>cert_4</name>
</filter>
...
</remove>
</certificate>
</packet>
2. With a single remove operation, you can delete certificates from only one repository which is defined with required webspace or admin node. In other words, you should use either webspace node, or admin node within remove operation nodes:
<packet version="1.4.2.0">
<certificate>
<remove>
<filter> ... </filter>
<webspace>site1.com</webspace>
</remove>
</certificate>
</packet>
or
<packet version="1.4.2.0">
<certificate>
<remove>
<filter> ... </filter>
<admin/>
</remove>
</certificate>
</packet>
3. With one packet, you can remove multiple different certificates from any of the repositories you own. To do this, use the required number of remove nodes in the packet:
<packet version="1.4.2.0">
<certificate>
<remove>
...
</remove>
<remove>
...
</remove>
</certificate>
</packet>