1. Securities markets.
The process of transmitting, reconciling and, in some cases, confirming payment orders or security transfer instructions prior to settlement, possibly including netting of instructions and calculating final positions for settlement.
Sometimes the term is used (imprecisely) to include settlement.
Outside the securities market, this process is generally referred to as clearing.
2. Tax - transactions.
In tax, a similar process to an advance tax ruling, also sometimes known as 'pre-clearance' or 'tax clearance'.
3. Tax - taxpayers.
In some jurisdictions, a written confirmation that a taxpayer's tax affairs are in order, issued by the relevant tax authority.