N.Y. Comp. Codes R. & Regs. tit. 20, § 53.2 – Transfers through a system for the central handling of securities.

(a) Transfers or deliveries upon the instructions of a depositor in a system for the central handling of securities (including the clearing and settling of securities transactions):
1. (1) established by a national securities exchange or association registered with the Securities and Exchange Commission of the United States; or
2. (2) maintained by a clearing corporation as defined in subsection (3) of section 8-102 of the Uniform Commercial Code, from the name of such depositor or his nominee or from the name of his customer or the nominee of such customer to the registered nominee of any such system, are exempt from tax when made for the purpose of holding such shares or certificates, as agent for such depositor. Transfers or deliveries upon the instructions of any such depositor from the name of the registered nominee of such system to the same depositor, customer or nominee are similarly exempt. (See section 55.2 of this Title for provisions relating to registrations of nominees.)
  (b)
3. (1) In the case of registrations of transfers exempt from tax under subdivision 5 of section 270 of the Tax Law which are effected through any such system for the central handling of securities established by a national securities exchange located in this State, or maintained by a clearing corporation located in this State in which capital stock is held by such a national securities exchange or by a corporation subject to supervision or regulation pursuant to the provisions of the banking or insurance laws of this State, a proper exemption certificate must accompany both:
  1. (i) the instructions of the depositor to such system or its nominee directing the transfer of such depositor's shares; and
  2. (ii) the system's or its nominee's instructions to the transfer agent, issuing corporation or trustee issuing certificates subject to tax under article 12 of the Tax Law for the transfer of depositors' shares.
4. (2) The exemption certificate referred to in subparagraph (1)(ii) of this subdivision may be either the exemption certificate of the depositor which accompanies the depositor's instructions to the system or its nominee or an exemption certificate made by the system or its nominee in reliance on the exemption certificate or certificates accompanying its depositors' instructions to such system or its nominee. A single exemption certificate by the system or its nominee, in reliance on the exemption certificate or certificates accompanying its depositors' instructions to such system or nominee, may be made with respect to exemption certificates submitted to such system or its nominee by one or more depositors.
(c) Where a broker, dealer or investment company registered under the Securities Exchange Act of 1934, as amended, or the Investment Company Act of 1940, as amended, certifies to its affiliated clearing corporation under section 52.2 of this Title that all of the entries in his account with such clearing corporation as reflected in a daily statement of transactions represent transactions subject to the stock transfer tax upon which the tax will be paid, and/or transactions which come within one or more of the exemptions specified in subdivision 5 of section 270 of the Tax Law, and that evidence in proof of each such exemption is maintained by the broker and is available for inspection by representatives of the department, such certification shall be deemed to apply to all of the transfers reflected on such daily statement which represent transfers exempt under any of the provisions of subdivision 5 of section 270 of the Tax Law.