The post-Hurricane Bertha mop-up started in the north yesterday as the aftermath of the big storm continued to cause problems for travellers.
There were no trains between the Highland capital and Perth and Aberdeen because of damage to the line, and flooding under the tracks at the Lossie viaduct in Elgin also halted services to the north-east.
At Kingussie, engineers were working to replace the track bed which had been washed away by the deluge.
Trains ran from Inverness to Nairn and to Aviemore, but from there passengers were taken by bus to their destinations.
Nick King, spokesman for Network Rail, said: “We have still got issues at Kingussie. A wash away and flood water has removed the ballast under the railway from the track beds and engineers have been working to replace the ballast this morning.”
However, Mr King said it was hoped the line would reopen today.
Meanwhile, a number of roads remained closed across the area yesterday, including the A836 Bonar Bridge-Lairg route at Invershin, the A938 Carrbridge-Dulnain Bridge and the A832 Kinlochewe-Gairloch at Kerrysdale.
The A835 Ullapool-Tore road, which was badly affected on Monday, was open to traffic under convoy as Bear Scotland tried to excavate debris at Leckmelm, south of Ullapool.
People travelling to catch the Ullapool-Stornoway ferry faced delays reaching the terminal.
Three areas were particularly affected – Leckmelm Gardens, Leckmelm Farm and Corrie Lodge.
Bear Scotland’s geotechnical engineer also assesses the forestry area where debris had fallen, although access was restricted due to dense undergrowth.
A Bear Scotland spokeswoman said: “Despite the constraints of the sites and continued wet weather, we have successfully removed 900 tonnes of debris from the site.
“Our efforts will continue into Wednesday when we plan to remove a further 600 tonnes of debris.
“Traffic will continue to operate via a convoy system overnight and through Wednesday and it is being arranged to facilitate the ferry timetable.
“Work is ongoing and we don’t yet have exact timings of when the three sites will be reopen as normal. We will endeavour to keep the public updated as work on site continues to make progress.”
Meanwhile, the Scottish Environment Protection Agency maintained 13 flood warnings in the region, the majority for the River Spey.
Farmland in Badenoch and Strathspey remained badly flooded although the waters had receded from their peak on Monday morning.
In Carrbridge, the River Dulnain was still rushing in torrents past the popular packhorse bridge but the level had dropped several feet overnight.
It was feared that the Grantown Show, which takes place tomorrow, would be called off.
However, committee member John Kirk said the event would take place.
He said: “We have lots of phone calls but the field is dry so the show will go ahead unless there is another major storm.”