A 33-year-old man is on trial in the District Court in Perth accused of involvement in a multi-million-dollar card skimming scheme involving customers of fast food company McDonald's.

The scheme led to a total of $3.5 million being taken out of the accounts of thousands of West Australians.

It is alleged Navaneeth Ponnabalam was one of many people who took part in the scheme, which involved swapping EFTPOS pin pads at McDonald's stores with ones that could record the bank details of customers.

The court was told customers who used the drive-through had details of their accounts copied by the machines and then money was withdrawn from their accounts interstate and overseas.

Money was taken out of their accounts in India, Britain, Canada and Malaysia.

Prosecutors said the evidence against Ponnabalam included fingerprints that matched his, being found inside one machine at McDonald's in Maddington.

The court has also been told that his travel between Perth and Sydney coincided precisely with the dates the EFTPOS machines were tampered with.

Prosecutors said Ponnabalam was living in Sydney but he made regular trips to Perth at times when the pin pads were swapped.

Ponnabalam has denied any wrongdoing and pleaded not guilty to 449 charges relating to about $800,000 of the total that was taken.

His lawyer told the court there was no direct evidence that his client had engaged in any unlawful activity.

The trial is expected to run for two weeks.