Motorists have been urged not to make any journeys in parts of the Highlands and Grampian as high winds and flooding continue to cause problems.
Thousands of people were left without power and 40 people had to be rescued from their flooded homes in Dingwall by lifeboat volunteers from Kessock RNLI.
Police told people not to travel in Ross-shire, Caithness and Sutherland due to the danger of falling trees.
The force warned that more heavy rain and winds of up to 80mph were forecast.
Police described the flooding, which is widespread across the region, as a major incident.
Northern Constabulary said it was dealing with more than 40 incidents where trees had fallen across roads.
These included the A9, which was closed at the south end of the Clashmore junction and south of Golspie due to trees on the road.
The 1612 BST train from Glasgow to Inverness was forced to stop after hitting tree branches on the line between Carrbridge and Inverness. No-one was hurt.
A line was washed away at Helmsdale, meaning that alternative transport will be required for journeys between Inverness and Wick for several days.
Highlands and Islands Fire and Rescue Service have dealt with more than 160 calls since 0900 BST in the Ross and Cromarty areas.
Storms have also flooded houses and premises in Kirkwall in Orkney, where most schools have been closed.
Police said 23 houses in Dingwall were without power and there were reports of failures in Lairg and the Black Isle.
Jubilee Hall, Evanton, and Dingwall Academy were being kept open as reception centres to offer people forced out of their homes temporary accommodation.
Local councillor and Dingwall resident Margaret Paterson said: "This is just so distressing and there are so many people who don't know where to turn to.
"Their homes are flooding and some have moved upstairs. We have tried to get people out of their homes.
"Elderly and young children have been taken up to Dingwall Academy."
Golspie and Fortrose were also affected.
Highland and Islands Fire and Rescue Service, Scottish Ambulance Service, Highland Council and roads agency Transerv are involved.
The Met Office has issued a heavy rain warning for the Highlands, Moray, Aberdeenshire and the Northern Isles.
Supt Andy Cowie, the officer co-ordinating with emergency services at Northern Constabulary's incident room, said small communities had been among the hardest hit.
He said: "The changing weather situation continues to give us some concern. However, all agencies are working closely together to try to ensure minimum disruption to people's lives."
Motorists were earlier forced to wait near the Cromarty Bridge in the hope that a closed section of the A9 would re-open.
Gavin Phillips, a supermarket duty manager, was trying to get to work in Alness but only got as far as crossing the Cromarty Bridge before he was caught in a traffic jam.
He said: "When I got here it was still dark and it looked like a traffic jam. The headlights of the traffic stretched all the way back over the bridge."
Linda McCulloch was also trying to reach Alness. She said: "I'm trying to get home.
"The police advised anyone whose journey was not necessary to turn back. There was a livestock lorry here and it had to turn back because the sheep were getting distressed."
Louise Palmer, who sent in video footage from her car, said they had struggled to reach Dingwall from Knockfarrel.
"Ditches have burst and can't cope. Fast flowing water gushed over the roads making it almost impassable," she said.
Traffic waiting for the A9 near the Cromarty Bridge to reopen
A landslide has also closed the rail line between Dingwall and Thurso and Caledonian MacBrayne has cancelled the Ullapool to Stornoway ferry until Friday.
Ken Humphreys, who runs a hill farm on the back road between Dingwall and Evanton, told the BBC Scotland news website that he had been virtually cut off.
He said: "There are several trees down, the top and bottom roads out of Dingwall are closed off.
"We have had continuous overnight rain the past three or four nights - it has been some of the heaviest continuous rain I can remember in 70 years."
Central Scotland Police has also reported some problems on the roads, including near Glenrothes.
Live flood warning information is available from the Scottish Environment Protection Agency (Sepa) on 0845 988 1188.
Left Dingwall this morning at 0645 for Ullapool. In and around Dingwall it is horrendous especially up off the Old Evanton Road. Several streets are like rivers.
Lots of branches and debris from trees blocking drains.
The road from Dingwall to Strathpeffer was especially bad around the Auchterneed junction bad with 2 feet of water over road. The Auchterneed road was like a spate river.
Left Culloden at 0710 this morning, managed to get to the Cromarty bridge but it was rather hairy all the way. Had to turn back at Cromarty as there was about 2 - 3ft of water on the road.
This appeared to be coming down the hill from Culbokie and was raging like a river!
Turned the radio on and heard the road was closed on the other side of the bridge anyway at Foulis.
I haven't seen floods like this since the severe ones in Inverness a couple of years ago and this certainly brought back memories.
So, an impromptu day off work which is all very well but no pay.. bah!
Caithness is shut. There is severe flooding on all roads - major and minor - and many roads are, at best, passable with extreme care.
All the burns are running bank full or have burst their banks.
A landslide on the A9 at Scrabster has completely closed the road for the foreseeable future.
The B876 Wick to Castletown, A99 Wick to John o' Groats and A836 John o' Groats to Thurso roads are all a foot under water in places.
At the moment, the wind has died down and things are getting a little brighter so, hopefully, the situation will improve by this evening.
At the moment the road between Strathpeffer and Dingwall is closed with buses and cars blocking the way.
At 8.00am the water was at the bottom of the car doors.
The fields to either side of the road are flooded and it may take some time to drain it.
The housing schemes behind the police station in Dingwall are flooded at the lower parts, with the water reaching the windows of the cars.
It is very interesting and rather ironic to see on the BBC's website that in Dingwall today the place of safety and shelter being used by the authorities for the victims of the flooding is the present Dingwall Academy building (to be demolished in 2008). The former Ross and Cromarty County Council very wisely chose in the 1930's to build on that site and not on the flood plain of the River Peffery below, which came to form its playing fields - now the construction site of a new PPP2 school.
Dr. John W. Grant
We're in the process of putting a roof on a steading - gale force winds appeared out of nowhere late afternoon and forced us to hastily evacuate the site, abandon our caravans and take refuge in the cottage next door. Even there didn't feel safe: a large tree came down a few yards away from the front door along with some hefty branches from other nearby trees. Lots of brief brown outs too...