When a cheque is deposited at a branch of a financial institution (FI), it will be sent for processing to a regional data centre serving that FI, usually that same evening. In most cases, before midnight it will be cleared, or delivered, to the data centre that acts on behalf of the FI that holds the account on which the cheque is written (i.e. the drawee FI).

Each Direct Clearer, or its processing agent, will first sort the cheques according to the Direct Clearer responsible for settling the item, bundle them for delivery, and enter into the ACSS the corresponding total number and value of the cheques to be delivered to every other Direct Clearer. To optimize the flow of cheques through the clearing system, several cheque exchanges are scheduled each evening at six regional exchange points: Halifax, Montreal, Toronto, Winnipeg, Calgary and Vancouver. Data is entered into the ACSS for each exchange.

In some cases, clearing a cheque cannot be completed overnight on the day it is deposited. For example, cheques that cannot be processed by automated equipment must be processed manually the next day. As well, cheques deposited at a branch on a Saturday will not be cleared until the following Monday evening, because clearing takes place only on regular business days. The clearing timeframe may also be for cheques deposited late in the business day or through an automated banking machine.

Once a cheque arrives at the regional data centre serving the receiving Direct Clearer, the financial institution (if it is drawn on an Indirect Clearer) and/or the branch holding the account on which the cheque is drawn must be identified. The cheque will be routed or "presented" to the branch of account, or the designated unit within the "drawee" institution, where it is determined whether the cheque will be honoured or returned (for example, for insufficient funds or a stop payment order). This process is commonly referred to as making the "pay/no pay decision".

If the branch of account is located in another region of the country, the cheque may be sent by air or ground courier to a data centre at the regional exchange point serving that location, and then delivered to the branch. Once the cheque arrives at the branch of account, in accordance with CPA’s Rule A4, the branch has until the next business day to make the "pay/no pay" decision. If the cheque is not honoured, it must be returned to the branch that initially accepted it on deposit, and this process must be initiated within the "next business day" window. The return journey retraces the forward delivery or "presentment" route and may likewise take several business days.