You can do it as follows:
> x<-c(2, 4, 6, 9, 10) # the list
> y<-c(4, 9, 10) # values to be removed
> idx = which(x %in% y ) # Positions of the values of y in x
> idx
[1] 2 4 5
> x = x[-idx] # Remove those values using their position and "-" operator
> x
[1] 2 6
Shortly
> x = x[ - which(x %in% y)]