Basically, all Estonian companies with a VAT number are obliged to file a VAT return. Download the KMD form and its annex here
VAT tax returns can be filed using the e-Tax/e-Customs online environment: VAT declarations on form KMD and an Annex KMD INF listing all sales and purchase invoices with domestic counterparties exceeding EUR 1,000 in one month must be declared on form KMD INF. Supplies of services to VAT-registered customers of other EU Member States must also be declared in the monthly EC sales list due by the 20th of the following month.So, in order to file VAT Return, a company must collect incoming and outgoing invoices, as they serve as a basis for the declaration itself and must be listed in the annex.
Outside of that, companies are obliged to store all invoices electronically for the next 7 years.