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ScotRail had a day of disruption across its routes, external on Sunday, but said the "vast majority" of services were expected to run as normal on Monday.
The operator said there had been speed restrictions on all routes, all day, bringing longer journey times and some service alterations.
The following routes were closed or facing cancellations:
Glasgow Central - Ayr: No trains operate between Kilwinning and Ayr.
Glasgow Central - Gourock and Wemyss Bay: Alterations to services.
Glasgow Queen Street - Oban / Mallaig: No trains operate between Fort William and Mallaig and between Crianlarich and Oban.
Inverness - Kyle of Lochalsh: No trains operate between Kyle of Lochalsh and Achnashellach.
Inverness - Wick / Thurso: No trains operate between Helmsdale and Wick / Thurso.
On Sunday night ScotRail said it was working with Network Rail's specialist weather team, who would carry out safety checks on all affected routes before passenger services could resume.
They have been clearing fallen trees and debris, and dealing with flooding and damage to infrastructure.
The operator said passengers should check journeys before travelling, allow extra time, and consider alternative arrangements where possible.
Passengers are advised to expect significant disruption and longer journeys, and should check services before they travel.
Gary Hopkirk, route director at Network Rail Scotland, said it had been a "really challenging weekend" for the railway.
"We know disruption is frustrating and we really appreciate the patience people have shown this weekend while our teams do everything they can to get everyone moving again," he said.
The airports at Glasgow, Edinburgh, Inverness and Aberdeen have all had flights cancelled during the storms this weekend.
Journeys to and from London Heathrow, Dublin, and the Northern and Western Isles are particularly affected, and some flights to other English airports, Belfast and Amsterdam also cancelled.
Edinburgh Airport alone has had 81 cancelled flights and reported 11 flights diverted to other airports since the start of the weather warnings on Saturday.