A scatter plot requires two axes:
plot(x,y)
it's not hard to script things in R to load lots of csv files and do something...
for ( file in list.files(filedir) ) # make a list of the files to load
{
tmpcsv <- read.csv(paste(filedir,file,sep='')) # read the CSV file
postscript(file=paste(file,".eps",sep=''), paper="special", horizontal=FALSE, onefile=FALSE)
plot(tmpcsv[,1],tmpcsv[,2])
dev.off()
}
Perhaps you could be more specific, and provide a reproducible example?